Yes and no. You can get single window or pairs from the manufacturer sometimes. It is usually too costly to be worth it though. I know Bestop has replacements readily available but as far as I know they only work on the Bestop tops.
There is no way I know of to replace only the clear plastic but you might want to call around to places that make boat tops. they might be able to custom make something like that but I'd expect it to be expensive.
Another option is to watch craigslist. There are often people selling Jeep windows and you can get some good deals if you're patient.
Your friend could also go ahead and buy his new top and then sell his old one on craigslist to help with the cost. If his top is good then it should get $100 minimum even with jacked up windows.
Home made TJ trunk with soft window storage and a sub-woofer: