The 200' rule is an FAA regulation. No way the mouse is getting around it. At best, they could figure out how to incorporate the light into the theme of whatever they are building.Every historical WDW book and article I've read cites the 2000ft max for a structure without a flashing beacon. Maybe that rule from the 60s(?) doesn't apply anymore, but that stuff doesn't tend to change. In any case, I can't see them building it any higher unless they could somehow mask the beacon from the ground view without disguising it from planes.
I wouldn't be opposed to Disney somehow getting it declared a no fly zone. At least that would keep the Jesus planes away. But I guess there could still be a stray plane flying over illegally, making a beacon necessary.
http://www.unimar.com/federal-lighting-regulations/
More detail can be found here.
http://www.faa.gov/documentlibrary/media/advisory_circular/ac 70 7460-1k.pdf