Which means that actual aliens would be . . . nothing human
I like a lot of what you say here, but I feel like the problem in the comparison with the conquests of the Mongols, Arabs, etc. -- apart from the equation of contact with a novel culture with being conquered by one -- is that those were situations of humans encountering other humans, so naturally it led to some expansion of the possibilities of how to live as a human. The aliens are by definition not human, so in order for this to create a dilemma they would have to be *just human enough* for people to somehow recognize them as peers, and therefore make use feel like they reflect on us somehow. I'm not sure where that line would be, but I don't think that tool using would be it; the differences that you bring up are moral ones, not technical ones, which is why we seem to live with some tool-using animals and robots without worrying about their morals. It does seem like "They act like I wouldn't, but they're not human" is always there as an escape hatch, because we've basically always done that with animals.