I can imagine how Torchwood would handle the Borg. Infect Captain Jack with some kind of super-nasty STD. Send him over to the Borg cube to charm his way through the ship, one drone at a time. The Borg sicken and die. Get Captain Jack back, give him the cure, have him get off a quick one-liner. Next episode.The best counter to this sort of illogical villainy is a bit of illogical heroism. Like if Starfleet decided to recruit Torchwood or something to build up some kind of fancy, clandestine silver-bullet defense that gets yanked out of the woodworks if the Borg ever show up again with whatever asinine scheme they've decided to use.
Hell, that's apparently what Icheb's parents tried to do. The fact that it worked as well as it did sorta proves my point, if you think about it: the best defense against the Borg is usually a half dozen sneaky bastards with some kind of silver-bullet technobabble weapon that strikes the Borg at their weakest point.