The Wahhabi madrassas emerge late in the book to serve as a contrast to the schools Mortenson is building. Even though the mindset is usually education = good, in this case, the education the madrassas give, one in militant jihad (19.24), = bad. They're like beehives that "brainwashed students" (19.31) into mindless drones to do the bidding of the fundamentalist rulers in charge.
Unlike real beehives, though, which we need to survive, we probably don't need these, especially if they are simply supplying entities like the Taliban with ready-made operatives. If this book has anything resembling a greater villain, these schools are it.