If planes would fall out of the sky after an EMP hit there is one sure way to get that radar hole fixed: Have all the airline companies refuse to fly until it’s fixed.
From http://aviation.stackexchange.com/questions/11266/which-airliners-could-survive-an-emp-pulse it seems like there are some planes that have manual controls that could be used to land safely, depending on when and where they were when the EMP hit. 727’s and 747’s are specifically mentioned as having manual controls. But finding a safe place to land could be difficult with no ATC, especially if it’s at night. If the fuel and/or glide run out where there are mountains all bets are off.
Maybe some pilots here could give a better idea of what would happen.