Is there a way to prevent Housecarls/spouses from sitting down in certain chairs?
There's an easy way, use fake chairs ... but then no one can sit on them (player included). Works though

Other than that ... not an easy one I can think of ...
You could, I guess, have a FormList of "unuseable chairs" that you scripted into an OnUpdate event for the NPC(s) in question ... Not that I can quite see how you would script it
Or, you could, I guess, put an OnActivate event in a script you placed on any chair that you did not want Karls to sit on (but that would be editting vanilla, I should imagine, which you may or may not be OK with)
Or you could go with Justin's idea (I still can't believe how quick the bloke types!!), but again, that might mean editting vanilla?