I agree, the problem with rounds dragging out has nothing to do with horse crossbow, it has to do with MotF needing to spawn at random intervals EVERY SINGLE ROUND. A round should never draw, ever.
I honestly am frustrated with horse crossbowmen because I can't do shit against them with my champ courser and balanced heavy lance. I can either block the whole way into them, or try to stab then and I get killed (my speed going right into their bolt).
I don't think they really need to be balanced. They have counters, the horse archer. It's just that not many people are horse archer these days (probably has a lot to do with the developers constantly nerfing shit, like archery, so now instead of horse archers you have horse crossbows).
Also, other horse crossbows can easily counter another horse crossbow...but since it's mainly SemenStorm banners who are the horse crossbows, they are always on the same team.
I think the other issue besides MotF needs to brought up: team balance. Banner balance is great, and I agree you should try to balance by banner (when possible), that being said, teams should be balanced evenly based on the equipment people have equipped.