I'm not joining in on the discussion on whether the strat is too strong. But I feel that your proposed solution is not compatible with what players expect from the game. Almost any explosion / AOE is either a full hit or no hit. Making an additional exception for bombers is not desirable in my opinion.
An alternative could be that the strat doesn't drop one, but four or more bombs. Similar to the T2 Cybran fighter / bomber - but with more AOE and damage. That way the target in the center will (typically) receive full damage, where as targets on the outer edges will receive less damage. And it will all match with the expectations of the player.