You can use joint compound over thinset to restore a smooth surface, no problem. How I've fixed a problem like that is by loading a 12" plastic taping knife with joint compound, and spread a very thin coat over the thinset. I then let it dry, hit it with some drywall sandpaper to get rid of the ridges, then repeated with another coat that I smoothed with a drywall sponge. I recommend a couple coats of PVA primer on the fix prior to paint, just to ensure the paint gets a consistent bite (and you can see any spot repairs you need to do).