I doubt a glass company would take this on. And a window company will want to sell you new/replacement windows. Unlikely they will take on this kind of task. On that note, the wood frame of the sash looks in pretty bad shape. Not sure of the age of the windows, age of the home, the importance of it looking and functioning well, or any historic relevance of those windows? Maybe grab a mid size flat head screwdriver and probe around the bottom rail of the sash. Do you have some really soft spots? New windows may end of being a better solution than paying someone to repair/patch?
As long as the sash frame is still fairly solid, this looks like more of a handyman project; chipping and cleaning out all the rotted pieces and replacing with a matching panel molding (glass stop), sealing, and then painting. Slow tedious work and some risk of glass breaking. Again, could be a can-o-worms, keep new windows as an option if that is in your budget.
And you still have to look at any factors as to why so much rot is happening. Is it due to age? Minimal overhangs of the roof? Rainy/wet environment? No matter what course you take to fix this window issue, it will keep happening.