You shouldn't be getting physical sanctifies on mages (except Herja who is somewhat borked up) unless they forgot to add that fix to the new mages.

As for effecting Flavius, well, if it puts an enemy beyond the 115 morale then it prevents him from being able to stop a first round Skill attack, but that can be accomplished by increasing the effectiveness of the morale rune in the first place. So its no big advantage. Morale sanctifies are the weakest of the sanctifies.