This happens all the time. Just take a wrench with one hand and screwdriver with another. Then grip the base of the standoff (the hexagon part, not the treads) with the wrench and you should have no problem bringing the screw driver to the other side to get the screw out.
I would also recommend that you tighten standoffs before mounting the motherboard with a wrench. It will prevent stripping and keeps your motherboard sturdy.