Plot is, generally, a bad way to restrict magic. If all magic is going to carry consequences, just keep it away from players.
At least, my experience is that having an ability that you're afraid to use is just frustrating; I'd rather not have the ability than stare at it and feel like I don't dare use it. Or it devolves into the player trying to figure out ways to protect against the consequences so that they can use the ability. This approach works much better in a narrative than in a game.
Within PF, I think the best options are to stick to the E6-E8 area, where spellcasters haven't pulled massively ahead (and other problems, like math breakdown, haven't started yet), and to selectively nerf or ban particularly problematic spells. Or to play a game wherein casters in general are banned (and not torture the players by throwing tons of casters at them).