Most commanders do have a high morale... But militia and so would be almost useless (even more so than at the moment) during assasinations. If they weren't available in too high numbers, that is, if they were expensive and/or capitol only, I think they wouldn't upset the game balance too much. You could also consider giving them lower Stealth value than is normal for assasins, to compensate, if you feel it would be too much.
Longish answer for a quick question. Well, it's the shortest I could manage.
