I think I would use plexiglass, or maybe polycarbonate, or something like that. Fairly easy to machine and not too expensive, yet relatively hard to break. Yeah,I know it scratches. I would try gluing it in somehow--maybe automotive butyl windshield sealer?
There has to be some way of making smaller laminated safety glass windows out of larger pieces. Have you researched cutting safety glass on the internet? I would wonder if there might be some kind of a bandsaw blade with diamond dust that might work with water cooling, but it might be WAY expensive.
Probably the best answers would come from a company that regularly deals with replacing flat glass windows in machinery. Would they work on your old glass? Hard to say. Good luck, it looks like a neat project.