More like a modification than straight removal, but split the imperium. Have the Horus Heresy sunder the imperium but not in a 'and half fell to chaos' way.

You have Holy Terra + Mars + Ecclesiarchy + Inquisition in one faction, deeply religious with lots of arcane loot they barely understand. They've got the imperial assassins, the sisters, the grey knights, and countless planets of guardsmen.

Then you have a some space marine chapters that did not bow to the high lords of terra and have their own personal empires with their own guardsmen style human forces. Space Wolves, Blood Angels and so on. They can have neutral to allied relations with the high lords of terra, but occasionally fight with them too. Some marines could consider the Terrans as holding their father hostage while spreading a false religion about him.

Towards the spikier end of the spectrum you have Alpha Legion, Red Corsairs and so on not aligned with Chaos but openly hostile towards those who remained loyal to the emperor.