There's a quote in the core rulebook (somewhere) which reads along the lines of
"We fight for Chaos that we might live for ourselves"
Crucially, it's attribited to a Captain Benoit of the 'Free Systems Alliance'.
That doesn't strike me as someone who's "Rargh! Blood! Skulls! Tentacles!" but someone who's taken one look at the Imperium from the outside and (quite understandably) said they want nothing whatsoever to do with the Xenophobic, Genocidal, Militant-Religious, Oppressive Dictatorial Nightmare of an empire.
If people want to play Black Crusade as the good guys (ish), a nice setting is a region of space with an Imperial Crusade thundering through it; burning anyone with a native religion that can't be twisted into the Ministorum's neat little framework, annexing every world it can lay its hands on and strip-mining every resource to feed its war engine, devastating entire worlds if its convenient....the 'heretics' need to make alliances and form some sort of power base capable of opposing the Imperium, including recruiting Chaos Marine mercenaries, learning to use the powers of the warp, persuading independent worlds to throw their armies and fleets into battle now, rather than saving them for its own defence....
In fact, you can play a pretty good Black Crusade campaign by more-or-less following the plot of Star Wars with the Imperium cast as the Evil Galactic Empire, Vader as an Inquisitor, an Imperial Battleship as the Death Star(s), and the rebels as independent worlds being overrun by a crusade.