The Emperor explicitly stated death to ALL xenos. There are "good" ones or "acceptable" ones, the stars belong to mankind only. Every alien race, even the ones openly friendly or helpful to humans were exterminated by the hundreds, so that the Long Night when the supposedly friendly xenos turned on humanity in its moment of weakness would never get repeated.
All the primarchs were totally on board with this. Supposedly enlightened ones who dabbled on statecraft and rulership like Guiliman or Lorgar(pre-koolaid) went town on eldar craftworlds trying to escape and killed them to the last and destroyed their soulstones without remorse. Hell, Lorgar did it AFTER the eldar helped him with probably only a few strings attached and without provocation. The friendly and paternal Vulkan burned eldar children alive when they tried to surrender him without a second thought. They virus bombed entire empires where the humans and aliens have coexisted, so the taint of the xenophile may never spread.
People tend to understand how much the Emperor fucking HATED the alien.