The Imperium is notoriously xenophobic, like the Empire x10000. I would imagine the Imperium would partner with the Empire to exterminate (not enslave) all alien species and then incorporate the Empire into the Imperium. Alien force users would be exterminated while human force users would be taken by the Black Ships to further server the true Emporer who sits on the Golden Throne.
Empire's still full of unsanctioned psykers.
Purge the heretic, purge the alien, purge the mutant!