Also, CT has an article called dissecting the deadlift. If there really isn't a practical way to squat, then some of those variations may have to do.
Also, don't forget about goblet squats, split squats, pistols (support yourself and/or to them to high box at first), and some of the other exercises mentioned here among others.
Unfortunately for you at the present, the only thing like a back squat is a back squat. Also, Mark Ripptoes program will no longer be the one he wrote if you sub back squats for anything else because of the importance of the back squat in his programs. The back squat is the foundation of his programs.
So you might need to find another program in the meantime and like landstorm said, get everything else strong so when you can do back squats you'll have a strong P-chain and back.