I got a set of helping hands, with magnifying glass, for pretty cheap from Jaycar.
The ones I have, have got a thick plastic coating over the jaws of the clips. They will still scuff the board if you move it around while clamped but it's not bad.
if you can't find one with protected clips, you could always put a couple of layers of heat shrink on yourself., that would work.
as fj said they come with plastic coating, however mine have been used so much that they have had heatshrink added and are due for more... the clips generally won't damage pcbs as long as you are not rough