I thought of a possible reason why they wouldn't do this. Basically, you've got two choices with the unbreakable vow ploy: Obtain a class of civil servants willing to give up their own magic to do the job (fat chance), or force the criminals to do it to each other. The natural answer is the latter right? Well yes, except the part where you have to hand a criminal whose crime was severe enough to warrant stripping some of his magic a wand and give him enough mental breathing room to perform a complicated, powerful ritual. Some of them are just gonna go along with it, sure, but you only gotta have one high-profile screwup before that kind of a policy is abolished.
Whatever theories we may have, most of them contingent on the defense professor being Voldemort and the one behind this plot (a conclusion Harry hasn't yet reached and which, frankly, there isn't enough in-universe or possibly even total evidence to make conclusive), it is NOT "obvious" that noone was meant to die. Draco almost died and if it was anyone except the defense professor behind this he was almost certainly supposed to die. Hermione was, as far as I can tell, being sentenced to life in Azkaban, which I'd rank about the same as killing her. If anything, it's obvious that this was meant to be a lethal plot and sets him pretty firmly on the "defect" side.
Morally he didn't do it, and maybe Quirrel even had a desire to kill her sitting on a back burner before Harry got involved, but her death was caused by her interaction with Harry. It is no stretch to say that there is at least one hypothetical sequence of actions Harry could have taken, even given knowledge at the time (not realizing she worked for Lucius or was an animagus) which would not have resulted in her death. Heck, doing nothing would have resulted in her not death.
That is the level of challenge Harry is taking upon himself. Not just to not kill anyone, not just to keep your hands clean, not just to save people when he can. He's declaring that if any innocent person anywhere dies and there's something he could have done differently to save them, that's his failure condition. You can't do that.
That said, I thought about it a few minutes more and it could be his resolution is really about knowing he doesn't know how bad the situation is. It's certainly possible to get through, say, a political power struggle with someone like Lord Malfoy without anyone getting killed. Harry considers it possible but doesn't yet believe that his opponent is Voldemort. If his opponent is Voldemort avoiding casualties is impossible. If his opponent is someone less evil (though still pretty nasty), and the scope of the conflict is much smaller, he might be able to pull it off.
Is it me, or does Harry's solution to this dilemma seem rather... half-assed? Ignoring potential the loss of effectiveness from his resolving to suddenly switch directions the first time things get bad, is he really going to know the first time someone dies as a result of his war? How will he know the difference? He's already gotten someone killed by his actions (Rita Skeeter, who he doesn't even know about) and another person gravely injured (that auror hurt by the rocket, who he doesn't know about but admittedly he thought the whole affair was a mistake afterward anyways). How about opportunity costs, the fact that if you handed me 100000 galleons demanding I save at least 10 lives with it I could hand you back 99000 in change. And that's before the "war" even "started"; hostilities are going to get more open and more direct from here. It's madness to think you can finish war, even a weird semi-geurella war like this, with zero casualties, or that you'll know about every one.
With the condition he gave himself anyone should be able to see that "failure" is a foregone conclusion. And there's very good odds he's not going to learn that what he's doing isn't working until he's racked up a far worse bodycount than one.
Personally, to me it struck me as something I would try on a group of first graders (provided I knew I wouldn't be sued) but not on a group of adults. They know it's just a game, and treat it as such, but nobody's going to refuse because to me that sounds like a very fun game (approached from the right mindset, anyways, and provided you make sure the audience doesn't take it too far. I'd probably hand pick people to "criticize" and make myself a member of that group so I could step in if another was being problematic). So they all do it, and they all think it doesn't matter outside the game, except that since it was so unusual a thing to ask them to do they're going to remember when you tell them why they did it at the end of the lesson, and they're not going to forget it anytime soon. Preferably do it when they would normally be having a "normal" lesson.
Harry's army is about four years too old for that angle to work, so I wouldn't expect much of the "training". I'd expect more from the entirely conscious chain of reasoning that they respect General Potter, and that he has them do all kinds of weird "training" things and an awful lot of them turn out to be good ideas, and that he told you outright that he thinks this is an important thing for you to try to do. But then, that's a conscious chain of thought, and by the time an issue like this hits conscious thought it's already passed all the lines of defense that matter. So I wouldn't expect much of it. But hey, he's already employing a scatter shot approach towards their weirdness training so if this one idea doesn't work out it doesn't cost him much more than the time it took him to plan the exercise.
"Ah!" Harry said suddenly. "I get it now. The first False Memory Charm was cast on Hermione after Professor Snape yelled at her, and showed, say, Draco and Professor Snape plotting to kill her. Then last night that False Memory was removed by Obliviation, leaving behind the memories of her obsessing about Draco for no apparent reason, at the same time she and Draco were given false memories of the duel."
Since that was the last theory Harry proposed before he switched from theories to lines of attack, and nobody fully shot it down (there was an objection, but the objection was just that it'd be difficult), I have to assume that was his working theory when he left the room. And I would not automatically assume that this scenario, which we know to be very close to the correct one, would count as "innocent" in front of a wizengamot led by the angry, racist father of the victim.
Personally, for anything except comedy I like to read moderately-long bursts rather than short snippets--when I follow works that update daily but have updates that are too small I often stop reading for a while on the assumption that when I start again later I'll have a juicy backlog to trawl through. (Part of me wonders if it's just a matter of how good the author is at finding good stopping points though). HPMOR updates are not that small, but with its plot-heaviness I think I still found that I enjoyed it better when I read entire arcs at once than when I read chapters as they came out. I even considered not reading chapters once or twice until the next existed.
Of course, individual chapters are healthier for my sleep schedule...
Personally my problem with Harry wasn't so much that he immediately assumed there was a trick (shouldn't get a probability of 1.0, no, but certainly a basket worth piling some eggs in) but that he assumed the truth would get her off. He never once stopped and asked Dumbledore and Snape "If it was proven that she had been tricked into doing this with false memories, but still cast the spell willingly and with her own hand, would the Wizengamot still convict her?" I don't even know the answer to that question, but I'd certainly ask before I assumed it was "no".
Especially considering how draconian the law is and how one of the two most important members of the judge/jury is not only the victim's father but someone already predisposed to dislike her (for what amounts to unapologetic and on-record racial discrimination). In advance I wouldn't have been surprised to see a show trial that blatantly ignored the evidence to get a conviction, though Dumbledore's faction was a bit too vocal for me to expect that with my current knowledge.
I don't think that "Lucius chose the exact same number as a stab against Dumbledore" is a very complex hypothesis. We already know that he knows part of the story and can reasonably assume he knows the whole story about Aberforth. So of course if the situation already demands that he hold someone on Dumbledore's side (sort of) for ransom for some obscene amount of money, on the assumption that it won't be paid, how could he resist rubbing that bit of salt in his nemesis's wounds?
It's not part of some bigger plan. It's not some fancy maneuver. It's just an emotional attack of opportunity aimed at Dumbledore, probably just for pride's sake.
My interpretation has been more that the 'dark' plans rely primarily on application of force (most often political rather than physical)--threatening, blackmailing, bribing--and trickery. They tend to work in the short run, but in the long run can poison his reputation (people notice how dark he acts over time) and have nasty side effects. For the most part Harry's dark plans are pretty clever, because his dark side is pretty ruthless and very clever.
If you take that definition for the plans his dark side comes up with, he actually started out with a light side plan (talk reason with Lucius, however undiplomatically) but resorted to a much darker plan B (force the issue via political loopholes) when that failed. Releasing the Dementor actually doesn't strike me as the kind of plan Harry's dark side tended to come up with, since for all its risk it doesn't really solve the problem or use his resources efficiently. It sounds like what normal Harry would come up with when very angry; the same normal Harry who was having happy thoughts about Guillotines right before the sorting.