Probably not the best idea for 2 reasons:
1. There's no easy way to attach the work to a glass base.
2. "Crashing" the head takes on a whole new meaning.
Truthfully, glass is really hard (relative to most metals), so even accidentally, lightly etching the glass has a tendency to wear out bits. But a bad crash has the potential to shatter a glass base.
Issue #2 is easily solved with a limit switch. You don't even have to hack the software to implement it - you can cut the enable pin on the pololu carrier (or stepstick) and wire a switch between it and Vdd.
Issue #3 depends on the application. If you're milling PCBs, you'll never want to go down all the way to the glass anyways. In fact, for most applications where Z-precision is required, you never really want to go straight through to the bed.
Issue #1 is the only "real" issue, at least in my opinion. I've got no solution for that one (hence the bizarreness of the idea). However, for "light" tasks with not that much lateral (tangential) forces, finding an appropriate kind of glue might do the trick. Something that has high strength in X and Y directions, but offers low resistance in the Z direction. A clamp of some sort might work too, although i must admit i can't figure out how it'd look/work from the top of my head.