You know, now that I look at it logically, this guy actually managed to kill people...I think that puts him up there pretty high as a villain character...
I'm not sure about that. He personally never killed anyone, despite shooting Natalie several times. Nor did he shy away from being near or in a combat zone. If I remember correctly, he even regarded himself as expendable.
He wasn't righteous, but the way he broke everything down into loss vs. gain and business terms was cool in it's own way. I also happen to think he made the right decision he regards to destroying the Plants before destroying Genesis.
Given how crippled the Alliance's space assests had become after the first firing, even if they'd managed to somehow destroy the Genesis, there was no guarantee they'd be able to follow up with the Plants, which would then simply build another Genesis. Compared to the Alliance that had lost their main base and most of their fleet, Plant was in a better position to win the war and kill everyone on Earth.
Basically, go after Genesis, maybe destroy it, but lose the chance to destroy Plant and lose Earth anyway.
Yes, he had an irrational hatred of Coordinators, but it's hard to say it impaired his own personal judgement in any particular way.