Jiggly's idea would be like the prizon locks in level 4 of the dark world in LttP - you have to push against them for a sec to open them up, but it doesn't actually use up anything.

And along these lines, how about a 'shutter' combo? It would work by waiting until Link had fully walked into the room, and then if shutters should be triggered, the combos would switch to the next ones in the list. Then, when the player did whatever was necesary to open shutters normally (i.e. kill all the enemies), the combos would revert to what they were previously. This would allow for fully freeform dungeons.