Apple have nuked a processor family before. They'll do it again.
"Make your applications work under our new processor, or lose our customer base" tends to be how they do it. I'm sure they'll try some automated fudging as well, but at the end of the day it's going to require Mac software devs to at least recompile for the new CPU, and probably changing any hand optimised assembly bits to make it work. They've got two years to do it, so I'd imagine any active devs have plans already. I'd expect the likes of Unreal and Unity to just add an option for the new architecture. If you're one of the dozen people playing WoW on a Mac, you can probably say goodbye to that...