The issue is the standard "The AI neither loves you nor hates you, but you're made out of atoms...". The Europeans did not desire to wipe out Native Americans, they just wanted land and no annoying people who kept on shooting arrows at them.
The native American thing isn't analogous to paperclipping because they weren't exterminated as part of a deliberate plan.
The alien encounter thing isn't all that analogous, either. It makes a little sense for paperclippers to take resources from humans, because humans are at least nearby. How much sense does it make sense to cross interstellar space to take resources from a species that is likely to fight back?
The ready made economic answer to intra species conflict is to make use of the considerable amounts of no-mans-land the universe has provided you with to stay out if each other's way.
If it's worth saying, but not worth its own post, then it goes here.
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