Pretty solid, only problem is that enemies don't scale with the player, so the player becomes too powerful quickly and it defeats all challenge.
The bees becoming completely inactive once you leave the room is a bit of a problem to since it makes it easy to cheese the game early on. If you can't fix that you can probably at least mitigate it by locking the player in the room while the enemies are alive, so the player can't move far enough away to deactivate the bees. Doing that might also help prevent a player from just running to the end. (Not that there's any reward to that though)
I do think the way you implemented the limitation was fairly unique. It could be expanded upon though to show that the tree is "alive". Maybe the tree has a health bar that acts as a timer, and if you don't kill all the bees you lose?