hmm.. i see why it some of it can seem unsettling but the guy wasn't very eloquent with describing the underlying spiritual implications of it.
I don't think it was trying to say that we are all bad or that He didn't come here out of love. If sacrifice equals the seed of life, Jesus sacrificed himself.. not for our physical lives.. we are already here.. then for what? our spiritual lives.
If you read a bit further then it talks about the way in which the bioweapon worked. It only activates through intent (which is why the andriod could touch it, he didn't have a soul.)
So it's implying that the aliens intent in wiping us out was hypocriticial, because the biowepaon wiped THEM out, meaning they are as capable as evil as we can be.
Because of the themes relating good/evil with self-sacrifice, it also showed that we are capable of good because the one character ASKED to be shot with the fire because he was diseased.
But i should add that i don't necessarily think things happened like that (though it is quite clear there is alien involvement of some form) and you certainly have the right to take a movie in whatever way you want, thats the joy of fantasy type movies