You probably could do that, but Black Crusade might not be the best game to run it under. If you're playing Black Crusade, then you are a heretic, at least from the Imperiums perspective. Most, but not all, will have some link to the Chaos Gods.
And, as the saying goes, the road to hell is paved with good intentions.
The Imperium is massive and monolithic. Someone wanting to free his world, his sector, they can't do it alone. They need a backer. So they turn to Chaos. They make bargains, with the best of intentions. Each action takes them that step further. Each decision, rationally made, draws them in that bit deeper.
Read the Eisenhorn trilogy, you'll see how it goes.
I think the 4 Tomes are good, but you'd want to be sure you want to play the game, and enjoy it, before getting them, otherwise they're not going to do you any good.