@Cyan:
The reason why Akainu is considered more despicable than Crocodile is simple.
Crocodile is a career criminal. He's a pirate, mob boss, near-terrorist all in one. Evil acts are to be expected from him, and he doesn't make pussy excuses for his actions.
Akainu is a marine. As a marine, he's expected to be a moral, upstanding officer as a contrast to the evil and criminal pirates, supposedly above committing atrocities like they do. However, he's monstrously ruthless, perfectly fine with blowing up a civilian ship in the off chance that a fugitive escaped on-board. Akainu is a representation of everything truly wrong with the World Government's rule and Absolute Justice in general: A nigh-unstoppable man who's can and will do anything to achieve what he sees as the "greater good", regardless of who dies in the process.
Well said. Also, look back toward the Marineford arc, at his comments toward Luffy and Ace. Never once does he say their names, just "Son of Roger/Dragon". I think, it didn't matter if they were Marines or civilians, or if Ace did become a Shichibukai. If he knew them and their past, he'd probably try to kill them anyways, just out of principal.