I suspect that this would almost certainly not work. Microwaves have a wavelength that specifically matches the dipole moment of water molecules. It's highly unlikely that the glue would happen to match that.
Edit: I guess you could try, but I wouldn't put just the stone into the microwave. Instead, add a bowl of water beside the stone, to make sure that the microwave has enough load. That way, even if neither the stone nor the glue absorb any microwaves, the oven won't get damaged.
Needless to say, I'd do this carefully, in short bursts, so you can figure out whether the stone actually gets hot or not. If it doesn't, nothing is lost; only the water will get hot.
I'm not even going to attempt doing it in the microwave. Sounds to iffy. And then there's the wife. I like sleeping in my bed