The pit marks make it harder to get the cleat exactly where you want it to sit when you are tightening them down. I was wondering if I put a thin layer of superglue over the pit marks in the area where the spd's bite the sole, would this firstly do the job and secondly, be safe ?
I've never had pit marks so deep that this would be a problem, although I can see how that would be the case.
Depends on what your shoe soles are made of. I would try De Sisti's suggestion, or, if you don't have a soldering iron, buff the marks very firmly with something smooth, like the handle of a butter knife.
I've had success smoothing out gouges on my rotomolded kayak with this method. It's a sort of combination of the friction heating and the smoothing pressure.