Easy, you use another balloon to grapple it, reduce lift, and therefore bring it down in a controlled manner. Of course this takes engineering and thought versus using a missile we can readily reorder.
Wonder how much time and money it would take to create a maneuverable balloon that could rise 80k feet and precisely make contact with another balloon (that may also have some maneuvering controls).
It's not about thought and engineering. If it was actually useful to do that, the military would've had no problem developing a solution like that. In fact, air to air missiles are infinitely more complex and engineered than any grappling balloon could ever be.
It's just that it makes no sense to build something that is completely useless, for a scenario that won't happen.
