>>718014484
In the first game they definitely were, sure. SE wanted alien tech from the Illuminate and basically Gulf of Tonkin'ed them to start the war, fighting the androids was crushing a worker's rebellion, and the bugs were purposely bred to be bigger and breed faster so more spaceship oil could be harvested and they lost control of them.
In the second it's more of a 'sins of the father' situation where the new conflicts with at least the Illuminate and Bots were started entirely by them and not SE. War with the bugs was entirely their own fault again in part for similar reasons as the first game's but also they probably let it get out of control on purpose for population control and distraction and things just kind of snowballed from there.

So still kind of the bad guys but comparatively less so than their enemies excluding the bugs (but that doesn't mean stop shooting them).