I was rereading my copy of Dark Heresy: Disciples of the Dark Gods and was reminded of the heresy of the Temple Tendency.
The "Temple Tendency" or "Temple of the Saviour Emperor" are the remnants of the pre-reformation ecclesiarchy which was purged along with Goge Vandire after the Age of Apostasy. It has quietly spread into the Calixis Sector and is not seriously suspected to be there by the local Inquisition. The beliefs are generally held by interconnected lines of noble families who act subtly to preserve their faith and gain influence.
My notion is that a rogue trader dynasty could be populated with members of the Temple, whether originally or through marriage with believing noble houses. A dynasty offers unique opportunities for the Temple, which I'm trying to hash out.
* Setting up colonies where the obvious faith is either very friendly to Temple concepts (church armies, church wealth, church power above all other adepta) or at least amongst the rulers. The main weakness is that since the Temple mainly spreads through family lines, discovery of a Temple colony would point a big sign at that founding dynasty.
* Transport of shade priests and pontifexes within and without the Calixis Sector.
* Bringing economic might (and actual) to bear on ecclesiarchy interests, who the Temple regard as heretics and usupers.
* Finding lost secrets of Imperial history which could aid the Temple's cause (example given in Edge of the Abyss, a graveyard world of interest to the faithful).
Any more notions?