Also, is this planet like ten square miles large or something? How much damage is the character doing to the planet as a whole? We all willingly pollute our own planet in a much more severe way to do nothing more than make our own lives a little more comfortable, and I don't think that makes us evil, either. Short-sighted, maybe.
The character is not supposed to die, they're supposed to be evil. The point of the game is that winning the game is evil. It's not saying humans on earth are evil, it's suggesting that maybe they are, or maybe we're the bugs, or maybe some of us are the bugs and some of us are the engineer. We also don't know the intelligence level of the bugs. They're smart enough to coordinate attacks, pathfind, target polluting and military buildings, and sense pollution, but it's purposely ambiguous.