Actually, they did the best they could with what they had, and what they were allowed to do. As they clearly said in the episode, putting a bomb in an actual flying plane at altitude is absolutely not allowed -- no one will fly it, and the FAA won't let it in US airspace. (and they don't have the budget to blow up a fully functional 747.)
In almost every documented case, the people blown out of the plane are either not strapped in properly, or their seat went with them. In every case I'm aware of where some nut does get a bomb on board, it doesn't rip the plane in half; it makes a small hole and the plane lands safely minus the bomber (who goes out their new hole) and maybe a nearby passenger or crew member.