Glad to see you are going to tackle this Ash. An edit like this is something I have thought long and hard about myself, but decided not to bother with, since I really feel the Dr. M ending just simply doesn't work, and if there is no way to fix that, there is not point in trying to save this film...
Not saying this to discourage you, but that is what discouraged me from trying to do an edit like this myself. Still, even with the botched ending, there is a lot of good film there, and many of your ideas stand to make it even better. For how closely this movie followed its source material, there were a lot of nonsensical "small" changes that really brought it down (Rorschach death, many over the top bits, extremely goofy musical sequences).
Good luck with this. I will definitely be looking forward to seeing what you come up with. And I'd love to see you successfully recreate the original ending to the child molester bit. You are right, it would be hard to do it without it screaming fanedit, but if it can be done, I think it would be quite an improvement. The scene was obviously changed to add some more over the top explotation film style gore, and it did it at the expence of a very powerful moment.
Also, I like your idea of adding the ending quote from the GN before the credits. Have you considered adding all the chapter quotes into the film? Not sure if it would work, but I think it might be kind of cool to divide up the chapters with a fade to black>white text with quote>fade to next scene. Again, not sure if this would work, or just mess up the pacing, but at the moment it sure looks cool in my head as I imagine it.