Just a small thought, and i like to know what others think of it.
In the wh40k universe the inquisition has absolute power, they can assemble and command fleets of the imperium and armies. So why not make it that during the missions, the player can summon in a squad of elite imperial guardsmen (only once each mission), their equipment will be based on the influence the player has in said system, so more influence means better equipment.
When summoned the squad will try to kill of the enemies in the direct vicinity of the player, and if survives start wandering around on the mission map. The player has no direct control over their actions, but it would be an alternative to reducing the elite mobs in missions.