Click-to-move doesn't disable your other movement options. You can still drive your "new main" with the mouse / keyboard in exactly the same way as you did before the old main died.

It's only when you click somewhere that it's going to get confusing. I die - and transfer control - alot in PvP and although I wouldn't usually want it enabled on any character I'm driving, it really doesn't cause me any pain once I remember to just not click other than to target