I'm watching The Assignment and it has me thinking, should they really have introduced the idea that anyone with the equipment can just kill all the Prophets whenever they want? It raises the question, why didn't the Dominion just shoot a big chroniton beam into the wormhole from the Gamma side? Can't disappear a fleet if they're dead.
Excellent question. My only thought is that the Keiko-wraith, being basically the same species as the Prophets, knew exactly how to configure the station to the right parameters in order to create the proper chroniton array - and it wasn't exactly an easy task even with that knowledge, since it required the Chief engineer working around the clock in order to make the modifications. One could wonder why the possessed Dukat didn't present a similar plan to the Dominion in order to kill the Prophets - but I suppose that the overall agenda for the Wraiths as a whole was to take over the wormhole, so the new plan of gaining a back-door to the celestial temple was used instead.
We don't really know for sure you can kill a Prophet this way. We have Rom and Miles saying it will, and the Pah-Wraith saying it will, but we only know for sure that it will drive a Prophet/PW out of a host. (As in The Reckoning.) For all we know, the Pah-Wraith that was in Keiko got driven out by the blast and said to themself, "Damn it, it wouldn't have worked anyway!"
I see three other possibilities: 1. The Prophets had witnessed a future and thus the plan to destroy them but they knew it would fail, so they remained in the Celestial Temple. 2. The Prophets -- having seen this future -- decided to leave the Celestial Temple. Or maybe leave one part of it. We have no idea how large the Celestial Temple is but the wormhole could very well be a portal into a vast non-linear realm. 3. The Prophets never saw it coming and only blind luck saved them. Perhaps their measures to imprison the Pah Wraiths are beginning to fail if the Keiko-Wraith managed to escape the Fire Caves.