sure, the non-cannon story might upset, to the point of blood tears, a few hundred fanboys (or be generous and say thousand?) but it's not them that make these movies a financial success, its the mainstream audience.
I look at it this way: you don't have to be completely faithful to the source material, as long as you respect the core idea. Not because the fanboys will get mad, but because the core idea is what made the work succesfull in the first place (assuming this is lasting work like Watchmen and not a book that sold 10 million copies thanks to a boob shot and was forgotten the next day). An idea that works and resonates with people is like a very delicate equation, not to be messed with. Stray from what makes this character/concept/whatever "tick" and the whole thing goes to hell.
In this case, I can't think of a way to make a sequel that doesn't betray what the original was about. Then again, someone found a way to reboot a convulted franchise like Star Trek without making its dedicated fans feel like what they saw before doesn't matter, so I guess anything's possible.
