Evolution is powerful, but that doesn't make it an intelligence, certainly not a superintelligence. We're not defecting against evolution, evolution just doesn't/can't play PD in the first place. But I'm also not sure how important the PD game is to this scenario, as opposed to the aliens just crushing us directly.

And as long as we're personifying evolution, an argument could be made that the triumph of human civilization would still be a win for evolution's "values", like survival and unlimited reproduction.

We follow a version of your meta-golden rule. Treat your inferiors as you would like to be treated by your superiors.

I don't understand how this rule leads to the described behavior. As written, it suggests that the aliens would like to be crushed by their superiors...?