It seems to me that Crake believes that in order for the human race to survive, it has to become essentially non-human. He is doing what he believes is necessary to save what he considers to be the best parts of humanity. Barring the methods by which he achieves it, I think that it is interesting to examine this motivation as it stands, outside of the context. Personally, I do not agree with what Crake considers to be the best parts of humanity, just as I don't agree with Butler's argument that the "hierarchical impulse" is entirely bad. Just like Butler would remove this impulse, Crake removes the qualities that make the crakers able to joke â€“ "For jokes you need a certain edge, a certain malice" (306).
Fundamentally, I don't think that human ambition is a bad thing. Ambition is what has allowed us to pull ourselves out of lives that, no matter how idealized, were still nasty, brutish and short. Ambition is what has given us all the technology, all the power over the natural world that we now enjoy. Ambition requires self-interest, it requires that little bit of malice that makes jokes possible. I don't think that we are human without ambition, and I think that the most damage that Crake inflicts upon the idea of Humanity in the Crakers is his removal of the entirety of their ambition. They don't want anything more than what they have. With that attitude, what will they ever create?
So then the question becomes: Is Crake's way the only way for the human race to survive? Is there something inherently suicidal about the way that we act? I believe that Crake saw it this way, and was tormented by his vision, even if he would not admit it to himself. When Jimmy visits him at Watson and Crick, he hears the dreams that Crake has every night, and the terror that this inflicts upon him (218). I think that this scene brings (ironically) a real humanity to Crake. He is struggling with his decision, whether he wants to admit it or not
Crake, in the end, is not more than human. His creations are not perfect, no matter how far from human he has pushed them. By the end of the novel, they have created an effigy of Sandman, and are thus implied to be on the way back to humanity (361). Crake's last gesture is not godly, or superhuman, but simply another act of hubris, assuming that he can distill humanity into its most perfect parts.
I think this idea is central to why it is difficult to classify him as good or evil. We know that we are imperfect, as part of the human condition. Improving upon this condition must be something noble. If it assists in our ability to survive, and it can be applied to the entirety of humanity in one fell swoop, then isn't Crake a savior? This impulse conflicts with our ideas about making fundamental changes to our humanity in order to survive. Is it worth it? Is there something intrinsically noble about the human condition as it stands that should not be modified, no matter the benefits? Even if we pull Crake's decision out of the necessity for the eradication of all living humans, it is still an impossible decision to make.