It doesn't hurt my back, but it does hurt my shoulders. It's all about posture. I don't keep my ironing board next to my sewing machine, but force myself to get up and move around by keeping it out of reach (plus I get a at least a little exercise that way). Also, I don't sew for more than about an hour and a half at a time, then go do some housework. If I sit all day and sew, I'll be in agony by evening.
Switching your foot pedal to the opposite foot would necessarily change your posture, but only until you settle into that new posture. When you do that, your back will start to hurt again. Moving around is a must--at least for me.