You can totally use crazy person logic to justify certain groups of the Imperium being okay with eldar (eldar of an unusually obedient and amicable nature, that is).
1. Psykers are described as being hated "as much" as mutants and xenos and hating the witch, mutant and xeno is often done all in the same breath. This does somewhat imply that if the hate is equal, then the potential for acceptance (not the actuality) exists.
2. Sanctioned xenos are a thing that RTs, at a minimum, can do.
3. Imperials collaborate with eldar with surprising frequency, which makes the Invaders' actions all the more inexplicable.
4. IG commanders can work with ork mercenaries and even vendors, and an (unusually obedient and amicable) is vastly less horrifying
5. The usual imperial protagonist reaction to nonhostile eldar is more "Oh great... THOSE guys... ugh..." rather than "RARRRGHH DIE DIE DIE."