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.
- While nice idea, given that furnace is at very least bigger inside and possibly just entrance to some other space, it is likely that they could survive. That is, if government doesn't take it as hoax, if homunculi are only limited to house, if they don't immediately kill people who bring bombs etc. Another interesting thought- homunculi have, according to prequel novel, deal with Catholic Church and possibly made similar deals with other groups such as Vikings. Given that it also establishes that all legends are real, and that much of folklore speaks about people respecting and giving offerings to fae so that they would take care of things such as land being fertile, storms not destroying cops, plants and animals being healthy, controlling rains and droughts, it wouldn't be far stretch to assume that fae have deal with government.