I mean, aliens aren't completely out of the question: there's rumours that Onslaughts were built to fight non-humans (which I should point out could easily apply to human-built AI, and probably makes more sense given the Domain's AI proscription), so it could be humans have contacted aliens long ago and almost completely destroyed them (or else modern day humans would at least know something about them). A storyline where an ancient alien enemy of humanity returned to wreak vengeance on the Domain, starting by disabling its Gates, would be cliche but workable.
Generally speaking though I dislike aliens in sci-fi (same goes for fantasy races), since most of the time you could swap them with humans of a foreign culture and it would make no difference to the story. And as others have said, AIs are probably more alien to humans than most sci-fi aliens. Hopefully the Remnants will have a bigger role to play in the future than just system guardians.