Your windows are going to scratch eventually regardless. They're replaceable. When they wear out, buy new ones. Ditto for the top itself.
FWIW, I run my Jeep through a hand-wash car wash (where college kids do the washing and drying) on a weekly basis, year-round, with a soft top. The top is original to the Jeep, which is a 2002. Apart from the velcro not sticking to itself as well as when it was new, the top still works fine.