Now reading Black Crusade, I hadn't seen anywhere where characters could be converted from the light of one of the other systems to Black Crusade.

I mean...would it be simply adding Infamy and transforming Fate points into Infamy points based on the Infamy score they get when switching sides?

My Rogue Trader party is one day going to run afoul of a Radical Inquisitor in the Expanse. They will destroy an artifact that can show you the past, whereever and whenever on behalf of the Blood Ravens in order to keep it from a variety of foes trying to blast their way into the temple it is secluded in. The Radical Inquisitor being one of them. The Radical Inquisitor responds by declaring the players and their Blood Raven allies heretics and leads an Orkish fleet to ambush them at the Breaking Yards. Anyways...a few scenes later, the players have a chance to confront this Inquisitor, but not without him having support from the Imperial Navy. So, they can fight and risk cementing their traitor status or work another way to clear their name with him. Becoming traitor may require fleeing into the Screaming Vortex or to some other hidden area.

[...]Radical Inquisitor responds by declaring the players and their Blood Raven allies heretics and leads an Orkish fleet to ambush them at the Breaking Yards. [...]

rofl humm Blodd Ravens declared heretical by a radical inquisitor and the navy is siding with the Inquisitor? I mean this is totally a RP event. Your players should be pulling on all their allies to have that IQ assassnated if there is not already 20 different IQ to try and kill him....

Using orks? The Raven shouldbe alreayd at is side, removing the skin one layer at a time...

Essentially the player flotilla is getting repairs at the Breaking Yard. The Inquisitor ship will show up with an Ork fleet behind him as in chasing him. He vanishes into the Warp and the Orks have a bunch of new targets. They are defeated, it is the Breaking Yard after all so the players are not alone.

The players move to chase the Inquisitor ship into the Warp and find a psychic mine waiting for them. It explodes, taking out the enemy ship's wake, and thrusts the players in the middle of a Warp Storm.

The Blood Ravens are with the players on the ship. A full company of greenish recruits, hand picked by the Chapter Master with Vet leadership. Note the events in Dawn of War have not revealed his corruption yet so all these men could be suspect.

Of course all this can change as I generally work on a series of possible events that could occur in the game months in advance.

Make sure the players keep a close eye on their gear

Its in there. Bringing X into Black Crusade and vice versa.