I think the prevention to skipping the puzzle would to make levels more linear (one path to the end), however I think the player creativity allowed by breaking the puzzle allows for rewarding player creativity. I'm not quite sure though on the punishment for dying. If you solve or perfect that mechanic I'd say the game would be one of the best lock-and-key puzzle games out there :)
If you make a more procedural level design that is self consistent with your level design, you could make a really interesting "infinite mode" with the wave closing in and trying to get further every time!


