To be honest, I'm usually not that bothered by superheroes using extreme measures in their fight against evil in and of itself. (Murdering people is often too much for me, though, unless it's somehow justified, either as an action or as a plot point - e.g. having some thematic significance, or the POINT is a chink in the superhero's moral armor.) However, I mostly found that movie's Batman to be terribly immoral because of his motivation for wanting to destroy Superman - just because he's too powerful. Being so overwhelmingly powerful is a physical aspect of Superman's nature. To want to kill someone because of a physical trait they were born with is horrendous and xenophobic. It's the exact opposite of being a hero. Ironically, Batman was still the best part of the movie even though his morals were atrocious simply because his personality was well done and Ben Affleck did a good job acting.
Anyway, this is an interesting idea for a fanfic challenge, though if I were do it, I'd have a different angle, as you can probably tell from my different perspective.