Witch Hunters and Warrior Priests should definitely be ancillaries.

On the Tabletop, Flagellants have no command, but a Warrior Priest to lead them would be cool.

I think Guilds for Regional Troops is a good idea. Maybe not for every region though.

White Wolf Knights, Hochland Long rifles, hellblaster volley guns would all be great regional troops.

How many units are you planning? I imagine this faction will have a pretty long list.

Spearmen, Halberdiers, swordsmen.

free company, flagellants

2, 3, 4, 5? orders of Knights?

crossbowmen, handgunnners, pistoliers, archers.

cannons, Mortars, hellblaster, rocket launcher

seems like more than the average, I suggest not too many types of knights, because they are identical on the tabletop and will be very similar in the mod.