Well of course one has to be careful not to play into the theist's hands. Which is why it'll be obvious that the characters are flawed. It really should be obvious from the fact that they make concrete plans to kill people…
Theists will see them as perfect examples of the typical evil rationalists, but there's really nothing I could do against that. (Even if it were made very clear in the film, they would just re-edit it…). So I don't care about that much.
As to your hope of failure, it probably will (mostly because I'm a rubbish writer, don't know any passable actors, and don't have any money)
That's what I'm aiming at. They only believe to be rational, when in fact they are as ideological and misguided as everybody else, although not as obvious. That's mostly owed to the fact that they're only two people, since the risk increases with every conspirator they would add. So they form an echo-chamber of their own, eventually spiraling off…
yes, basically.
The distribution of their videos is supposed to spread it though, they hope to create a movement so no future church official could be save etc. Their discussions about if this would even make any sense and trying to find out who really holds power in the church (& the weak points), and if there is even a way to commit a "perfect assassination" of such high profile targets, would be the series.
They waver though. Through failed argument they arrive at a point where they think it's a good idea to plan their assassinations. The discussions about ethics and how they could actually execute their plan in a way that really increases well-being (they think there is a way to do it), i.e. without ending up with the theists uniting and rationalists outlawed. Their ultimate goal is getting rid of supernaturalism and especially using it for oppression (which would be good, I think most would agree). Having read about ethics a bit though, they come to the conclusion that killing some people would be outweighed by the danger to the future of humanity their victims pose.
They could consider deception, too. Stage a high-level hidden religious war, more focused than current religious terrorism, in the hope that society would blame religion if they see that all religions are guilty etc.
Brilliant!