In my experience, to wipe out a horde, you need to kill off the family members, which isn't as easily done as it is said. For starters, a general with the Night Attacker trait is incredibly valuable. It allows you to just pick on one army out of a mass and kill it, but you have to be certain to finish off the generals completely in the battles. Many times I've had one or two members of the bodyguard manage to make it off the field, and the bodyguard comes right back within a couple of turns. Assassinating them is great, when they have traits that make it easier and you have assassins good enough to do it, but that combination is rather rare.

I read a strategy that I found rather silly and cheesy, but effective, for dealing with the last city of a faction that will go into horde when you take it. The idea was to assault the city and kill off the generals, then deliberately lose the battle. Withdraw after their family members are all dead, and the faction will be destroyed. At that point you can capture the city from the rebels. Otherwise, taking the city just brings up a new horde.

Another possible tactic is attrition. Make mass numbers of cheap troops under captains, and go fight. Don't worry about winning or losing, just kill as many enemy as you can. As long as the fighting is in the field, you aren't losing anything, and they are getting weaker.