Could the Keeper remove darkness token from room?
Or remove any token from room?
The keeper can not remove fire/darkness tokens from the board. Even if he just spent his last fire token elsewhere and wished to take another. I don't have the manual with me but I'm pretty sure that somewhere on the last page it states that fire/darkness tokens are limitless.
A fire token can hurt both the investigators and the keeper's monsters. If the keeper could remove them, he could simply do so for his minions to avoid fire and renew the tokens whenever it is in his favor.