>Now, having some religious strife within the coalition sounds pretty cool.
It sounded like the Coalition needs something ongoing that draws their attention internally. Because it's not an external caused problem, the Cabal doesn't get involved.
The war is probably an ongoing thing now due to their FTL being slow, unless some other Client gets involved.
Let's see...
The Deviates are the supposedly original Chaos-controlled faction, accused of Grand Heresy and Sedition. At the Inquiry held by the Pontiff, they seemed at first willing to negotiate their theology and explain, but it ended up with the Pontiff and many high-ranked Deviate leaders dead, pushing the Deviates into open rebellion and the Sacristy declaring the Deviates as Apostate.
The Sacristy (The ruling council) then proceeded to have a multi-factional deadlock for electing the Pontiff, with the the Deviate members of the Sacristy expelled. Due to legal manuvers and support of the established, a Pontiff was eventually elected.
However a sizable minority of the Aggemar were upset over the underhanded but legal manuevers used and declared themselves in Schism with the intent to Reform the Church. Both the Reformists and Orthodoxists have declared each other apostate.
The Orthodox are the majority of the Aggemar, but are somewhat hampered by their legalistic religion and traditions. (Think: Catholicism)
The Reformists are slightly less hampered and more streamlined, and are the second largest Aggemar faction. (Think: Anglican)
The Deviates have tossed much of their religion aside. They have the core tenets, but have radical interpretations of them and are far more innovative than either other faction. However, they only have two or three worlds out of dozens. (Think: Protestant/Hussite).
All three factions accuse the leadership of the other factions of being in league with Chaos. If it's the case, then it's only the various warp-strong leaders.