I've been running Black Crusade for a while now, and have known about it for over a year (I was writing the psychic power rules this time last year), so hopefully I can provide some insight.
Broadly speaking, I don't personally see how a starting group can effectively work within an established Imperial settlement - while individually potent, putting them inside the Imperium limits a group's available resources and hinders their ability to gain more, beyond any considerations of character archetypes. The way I've chosen to structure my campaign is as follows: the player characters start with only the gear on their character sheets, on a world in the Screaming Vortex. It's up to them to gather resources and muster a warband (by any means necessary) to wage war on the Imperium or do anything else they want.
Black Crusade, like Rogue Trader, works better player-driven - the players are an authority unto themselves, have the freedom to do as they please, and the responsibility to seek out the things they need to achieve their own goals. If that requires spending some of their time infiltrating a hive city in the Imperium, then its the players' choice and its the players' responsibility to figure out how that'll work. While you can run the game as the opposite of Dark Heresy, that only really covers a portion of what you can do with Black Crusade, and freeform sandbox-style games, with the players defining their own goals and the means they'll use to achieve those goals, strikes me as the surest way to cover as much as possible.
In particular, the rules covering Compacts demonstrate an "everyone gets their moment in the limelight" approach, where the overall goal of the group (the Primary Objective of the Compact) is achieved through multiple distinct secondary objectives, which may be tailored to different elements of the group's strengths, so that different characters have the chance to shine in achieving different things.
And remember, characters begin mutating fairly quickly (10 Corruption for the first Gift of the Gods), so blending in with society isn't all that easy for human characters either.