Currently the Ostheer carpet bombing skill and Soviet god of war skill cannot be used on enemy HQ territory. But U.S. 105mm or Wehrmacht firestorm and V1 skills can be used on enemy HQ, wiping out those retreaters, providing lots of entertainment.
So I think all those skills should be able to be fired on enemy HQ sector.
About the balance, I think V1 is almost as devastating as god of war or carpet bombing, and you can continuously bombard enemy HQ with U.S. 105mm skill if you have enough munitions, So I think allowing them on HQ won't be troublesome.