Lexan has UV-resistent properties, but it won't stay clear forever. Covering it with a clear UV resistant material (like paint or UV blocking tinting film) can help. But, paint and flim can scratch. Not practical for something that is removeable or handled.
The real reason this will never happen (not from an OEM perspective anyway): Emergency responders can easily punch through safety glass to pull you out of a burning car. They can't do the same easily through Lexan. Lexan is the materal jet fighter bubble canopies are made of.
FCA doesn't want to make the panels with glass because of these possible reasons:
1) cost; it would put the Renegade at an uncompetitive price)
2) weight; glass is not light and the added weight would impact MPG figures... plus, it would make the Renegade more top-heavy.