WMG: Don't be Afraid of the Dark
The final scene is a false hope for the fairies.
Armed with the groundskeeper's testimony after he got better, and a few photos that they could find that showed the fairies, and the 1-2 dead bodies they went to the government. It turned out there is a precedent for this sort of infestation to kill off the fairies. The government drops a flashbomb or two into the old furnace immediately after The father and Sally leave the grounds. And just for good measure destroy the house - the cover story is a gas explosion - but the fairies are no more.