I propose that sheets of translucent plastic be used as windows. This would be installed as a big roll above and below the window. The sheet would be thin but tough, like Saran Wrap. Maybe you could even use Saran Wrap. It would be gripped at the two sides by long rails.

When the window was dirty, the side clamps would be opened and a crank turned. This would roll up the old window onto the bottom roll, and clean new plastic would unroll from the top. The clamps would be redeployed. When the bottom wrap was full it would be sent back to the factory to be recycled, and a new roll installed. The same people who install those cloth paper towel rolls would take care of these windows.

These windows would be more resistant to thrown rocks, and would be somewhat elastic, and thus easier on confused birds. Additionally, folks who wished to make blowfish could make sure the window was clean.