My 90 300E 2.6 is essentially the same car. When I did the blower motor, there was no real danger of stressing or cracking the windshield. I didn't even use tools to take the trim pieces off, they just pop out.
It's possible that they dropped a tool near the edge. It seems like a very suspicious coincidence, however it would be tough to prove anything in this case. Sorry, that's a bummer.
On another note, I'm surprised that they charged you the labor for the R&R on the blower when it was a misdiagnosis. The blower motor can be checked by applying voltage without any disassembly. Was it their misdiagnosis, or did you specificaly ask them to change it based on your own diagnosis?
Experience is something you don't get until just after you need it.