I agree, it can pretty rediculous what hoops Xenophiles have to jump through to integrate their alien neighbors, especially as you talk about primitives. It's even more ridiculous if you are a Xenophilic Militaristic species, i.e the people who should be enforcing alien tolerance with an iron fist.
I generally don't like restrictions based on ethics, though the flavor might change with the new political parties mechanic. However, I'd rather all ethos' be allowed to perform any activity, but have consequential events that question their choice.
Realistically, a xenophiles, ESPECIALLY xenophile militarists, should bringing the hurt on to xenophobic primitives (i.e aliens invade during WWII SPECIFICALLY to defeat Nazi Germany). Xenophiles should be able to infiltrate administrations to encourage pro-tolerance sentiment (think DIMA from Fallout 4 Far Harbor). However, somes choices WOULD realistically be dubious for a xenophile species. Rather than restricting a xenophile's ability to infiltrate or conquer, events could pop up like "Our recent conquest of [Planet] has been met with mixed opinions back home, with people arguing that we are no different from the errant souls we attempted to 'liberate'" and give the player the choice to say "yes, this is wrong (change law to not be allowed to invade or infiltrate primitives to please the population with a loss of influence)", or "Evil prevails when those who can don't act! (anger population, gain influence, and encourage militarism if one isn't militarist already)".
Xenophile militarists should not find any moral debate involving "liberating" primitives as long as they get treated like equals afterwards, though I'd imagine them still being upset with invading a "nice" race (fellow xenophile or pacifist), and using heavy bombardment (fearing collateral damage against innocent lives when their targets are very particular; light bombardment is fair game). Neighboring races can still dislike you for invading a primitive, because there are many reasons to (fanatic purifiers hate xenophiles consolidating power, pacifists believe inaction is better than violence regardless of how righteous it is, individualists believe space nazis deserve independence and life as much as space buddhists, etc.).
In regards to infiltration, there should be no moral qualms with infiltration just based on how vague the concept is. I mean, yes, it is specific in that you infiltrate the administration, but xenophiles should be pulling that off to encourage tolerant leaders to get in power ahead of the perceived "hatemongers". Indoctrination BETTER be an option for Xenophiles, because it makes no sense for xenophiles to not be able to proselytize their belief in tolerance and equality.