The problem, as I see it, is that there's simply no way to balance control heroes short of removing SE/Fury runes (if that even solves it).
Before BD (and if DH is released with energy block), everyone's line revolved around getting your Medusa to fire first. Medusa, Moon, Cyclops + 2 (witch, kraken, ninja?).
In the current state, BD's energy drain gives people options other than simply Medusa, which is why we now see burst teams (generally involving Ninja, Bard and adding on some others like Witch, Kraken, Plant, etc) in addition to Medusa teams. The hope with the burst teams is that you can kill the enemy Medusa before it can stone you.
If DH's shield blocks BD energy drain, then we're back to square 1 where the only line worth having involves Medusa, DH, Cyclops, etc. Except this time it will be worse because of Dungeon Man.
If they made DH's shield effect only Control heroes rather than all disables, then this would lessen the concern about Megataur, Cutie, Satyr, etc. This would also bring even more possibilities into the fold (theoretically) for heroes, because everything wouldn't revolve around Medusa anymore.
Control heroes are simply more powerful than everyone else and I don't know how they fix that.