Well, the ship's senior crew is turning heretic (specially the Arch Militant) and I think that at some point they will vent the RT and the Missionary through an airlock at some point.

I wanted to teach them a lesson and make them a little bit more God-Emperor fearing.

In terms of play, they are just boarding the Light of Terra in "Lure of the Expanse" and I have made it into a (costly) salvageable Repulsive class Grand Cuiser (the one with the "Cursed" characteristic). I never read Black Crusade but maybe I could get something from there?

Ideas please (the evilest the best, let's say I might want to exchange a live for the Grand Cruiser itself if they really want it for them). >

Well it depends on the brand of heresy, really.

If they're dealing with daemons, let them. And show them exactly how dealing with daemons usually turn out.

After experimenting with mutineers and causing horrible warp-tainted mutations to each. (and burning all proof afterwards)

They now have 3 different types of xenos in the ship, considering their last engagements and crew losses, their human crew now composes only about 2/3 of the total. (Mekboys helping the Engiseer, Kroots the Arch Militant at quelling riots, renegade Eldar corsair serving as advisor for that same Arch Militant)

They also have an heretical self-aware cogitator core stored in a box with a power field around it preventing its machine spirit from speaking to others around it.

I was thinking of adding a great unclean one in place of the Pale Mother in the Light of Terra endeavor. hmmm

Edit: like Ulkair in Dawn of War II, Chaos Rising (where can I find stats for this one? and also on other Nurgle minions' modus operandi).

For easy port (if you can say that) Well easier than from BC stats if your using "pure" RT rules.

Great Unclean One - Deathwatch: Mark of Xenos p.102

Plaguebearer, Nurglins - Deathwatch: Rising Tempest p.134

Beast of Nurgle - Rogue Trader: the Koronus Bestiary p.118

The Carrier, Daemon Prince of Nurgle - Rogue Trader: the Navis Primer p.138

I have one player in my group who is playing super-pious, which is difficult given the levels of heresy going on in the party. He's the Navigator which gets around the awkward "Throw him out the airlock" problem, but this is a bit of a solution because obviously heresy gets better stuff.

After refusing to accept help from a Xenos, even in the face of death at the hands of a Herald of Slaanesh, I gave him the option to buy Pure Faith as an Elite Advance, and a new Faith Power every time he did something suitably awesomely Emperor-fearing.

With Faith and Coin coming out you could also have your loyal members recover an ancient artifact of a long-dead saint, but if your heretic characters tries to use it have it just not work for no reason.

The interaction between crewmembers with differing personalities is one of the best parts of RT. I like when we have players running the gamut from pure heretics/teks to super-pious Emperor-worshipers. It makes for nice conflicts.