I would guess that the True Ending involves the Confessor stunning Akon. The aliens used every trick in the book to influence the humans. They communicated using real-time video instead of text transmissions. They gave speeches perfectly suited to tug on people's emotional levers. Since the Superhappies run at an accelerated rate, this also forced Akon to respond before he could fully process information.
I would almost say Akon's mind has been hacked. Akon had very little time to think before accepting the Superhappy terms and he currently seems resigned to the destruction of humanity. He uses "negotiations" to describe the Superhappy ultimatum. Anyway, he's probably not fit to lead the ship. The Pilot hasn't had a mental breakdown, he's just (understandably) outraged at what's going on. If the stunner is only used in the case of mental breakdown, the Pilot will have to be stopped by other means. Once a new leader is elected/promoted/whatever, the Confessor should require all real-time communication from the Superhappies to be text-only.
The Superhappies may be technologically superior, but their weakness is the fact that they don't separate genes from memories. They also don't withhold information from each other. This could allow a specially-crafted memory to disrupt or destroy the entire race. Even the kiritsugu are shocked by the slightest display of suffering, so it's not much of a stretch to say some images exist that would permanently traumatize all Superhappies.
Of course, destruction isn't the goal, modifying is. Before the Superhappies leave, the humans should ask to stay in contact with one Superhappy ship during Operation Babyeater. By studying them more, the humans could find a way to insert a memory that changes Superhappies to be less of a threat. If the humans have the upper hand, they can actually decide whether or not to adopt superhappiness instead of having the choice forced on them.
If it doesn't work, at least the humans will know how big the Superhappy armada is. They could wait for the Superhappies to return from Babyeater territory and blow up the system. The babies would be saved and humanity would be safe until the next nova.
Full cooperation is not one of the scenarios I outlined, since most humans would not want to become Superhappy. As the Confessor said, "You have judged. What else is there?"
Z. M. Davis: OK, well it may not be self-replicating but it was worth a shot. Extreme empathy is basically the only weakness the Superhappies have. I'm not a big Star Trek fan, so I haven't seen the first two episodes you linked to and I only vaguely remember the last one.
51a1fc26f78b0296a69f53c615ab5a2f64ab1d1e: Or early versions of the translator failed to convey the humans' stress to the Superhappies. The kiritsugu are rather isolated from the rest of the crew, so while they have knowledge of the Babyeaters, maybe they haven't seen the videos. It would be analogous to reading about the Holocaust versus stepping into a holodeck depicting a concentration camp. Yes, I'm assuming aliens have a bias similar to humans. If that's not the case, then all non-kiritsugu Superhappies will be grief-stricken for quite some time after hearing about the Babyeaters. There would also have to be a very good reason why kiritsugu lack an emotion/reaction found in the rest of their kind. Humans without empathy are autistic or psychopaths. Again I'm arguing from a human analogy, but removing an emotion can completely change a being (http://www.overcomingbias.com/2009/01/boredom.html).
Anyway, most of my speculation is probably wrong, but the main point I tried to make in my previous post is that Akon's leadership is seriously compromised. The Superhappies are very manipulative and the Confessor needs to get a handle on things before saving humanity gets any tougher.
Did I mention a holodeck? Ugh, curse you Star Trek.