Warhammer 40k: Dawn of War - Dark Crusade
They just wouldn't, they swear to serve the Emperor and defend the peoples on the Imperium, they wouldn't be so petty as to destroy Imperial forces because they were 'in' the way. It's simply relics way of fitting both sides in.
The Soul Drinkers are not actually "Excommunicate", they are "Rogue" or "Renegade", they do follow the Emperor, but they believe that Imperium has betrayed everything the Emperor stood for and must be destroyed for the good of mankind.
They have not devoted themselves the Chaos, they despise the Ruinous Powers as much if not more than they hate the Imperium that cast them out.