Eric,
First I'd like to thank you for a fascinating thread. My sympathy goes out to the victim and his family.
Everyone seems to have focused on bad code. What if the spindle for some freak reason went to an un commanded rpm? Memory or component failure could cause such a situation.
If the potential exists to punch though 2.5 mm of metal then the MTB should use thicker metal. I've had to hammer out doors on cnc's from stock leaving a chuck from cracked inserts, inserting casting for wrong part that looks about the same size, program error, ect.
All of our machines have automatic door closers so door weight isn't an issue.
As far as the windows go. you stack up layers, put in guard bars or put in a camera system. Windows don't last forever. On machines that don't have crashes, the flow of chips erode the glass to the point you can't see in there at all and the glass / acrylic sandwich has to be replaced.
Our Multiplex's don't get a year out of windows due to chips flying at them.
The bottom line is that guarding should protect the operator from a 'chit happens' day. You can not for see everything.
Wes S