I don't think a Harmony player who befriends the aliens should be punished in any way for doing so.
Of course not, but Harmony had nothing to do with this.
Sure, there's trade-offs and things, which generally boil down to "you can't settle this small part of the map", but
a) the AI can't settle there either unless they wipe out the horde of aliens,
b) they were only a barrier against movement because Frenzied Aliens made them spawn in greater numbers (not to mention the landmass was smaller than usual), and
c) 50 turns and "trade-offs", even if it's uncommon to be able to absorb a nest into your territory, is
still a small price to pay to essentially neutralize the alien threat (which is supposed to be significant for at least a couple hundred turns) for the remainder of the game.
Call me harsh, but I would only allow blue alien relations to Harmony players of a certain level. Needn't be too high, but it shouldn't be something you can start working towards from turn 20 without significant investment into understanding the aliens (i.e. non-afterthought Harmony levels/tech).
Purity profits from their destruction, and would generally be disdainful towards the aliens at the very least, so it would make less sense for it to work toward complete peace with them. Supremacy, on the other hand, could easily pull this trick and not have to deal with them at all for 70%-80% of the game: no intrinsic profit to gain from killing xenos (unless they make it their mission via Might), and no critical resource existing under their nests.
So all in all, too much controllability. You shouldn't be allowed to take the aliens for granted unless you devote some real, conscious effort to it.