Well, I think Joe wasn't thinking about how this will alter the future, rather than assuming this would kill two birds with one stone. By sacrificing himself out of existence, he believes his future wife would be spared and the lives of Cid and Sarah would change into a positive outcome (possibly).

I believe the ending had to be bittersweet, and not exactly happy in a traditional movie-sense. Nor was the film actually ABOUT time traveling, instead more a about vengeance and sacrifice with time traveling being used as a method of telling the tale of these moral ambiguity between them.

I personally loved it, but I can understand if anyone else didn't.