Ok, I have your problem figured out, mostly.

In export_descr_character_traits.txt there are three trigger that effect this:
Trigger agents5 (LeaderOrderedSpyingMission)
Trigger agents8 (LeaderOrderedAssassination & MissionSucceeded)
Trigger agents8a (LeaderOrderedAssassination & not MissionSucceeded)

All of these have a chance to give points in DeveiverVirtue and StrategyDread to your faction leader.
agents5 will give your faction leader (100%) chance a Spymaster ancillary.
agents8 will give your faction leader (100%) chance an AssassinMaster ancillary.
agents8a has a 10% chance to give your faction leader an AssassinMaster also.

Lowering eliminating the percent chance for DeceiverVirtue and StrategyDread will help stop your faction leader from getting dread from your assassination and spying missions.

Enjoy, this will allow my Lithuanians to kill off all these pesky catholic priests in my regions will still retaining "-the Chivalrous".