I can easily visualize the mostly permanent card as something that can be exploited.
I agree. I mostly was just trying to get it down on e-paper while the thought rumbled through my head. I think what actual playtesting would reveal is that some combinations of command cards and units are too good. I am thinking that what would likely happen is that certain cards would be allowed for Legendary Units and certain cards would be allowed for heroes (or individual heroes would be represented by certain cards).
I could see a certain faction card that had a really faction specific feel to it being applied to a hero and then that hero might run with a different faction and impart that factions feel to its unit. You could have a goblin slave that escaped from his Dwarven captors and now allows a unit that with which he is associated to use one of the dwarven Rune cards.
Again, just thinking while I write...