Thinking it over, given what we know of Zod pre-phantom zone, I really don't see why he should be so villanized. (Post Phantom Zone, Sure, probably made him crazy)
I mean, the entirety of Krypton would die with no survivors if nothing was done, and the Science Council wasn't even considering the possibility of Krypton dying. A coup might have been a bit extreme, but was it really out of line considering what was at stake?
I do genuinely think that with the information we've been given about Krypton and Zod pre-destruction, he was actually in the right. Something needed to be done, and the Science Council wasn't doing it.