Lots of people remove the windows. Lots of people don't.
Personally I like the windows as does my wife hence why we got a school bus.
Like you said after taking them out and cleaning them they might work. Or you could always seal them shut permanently. Also Jake Von Slatt has a video on dissembling the windows and reversing them. Might be able to clean them better that way as well.
As far as insulation/sweating goes I would insulate the bus as best you can in every other spot. Then get a good black out curtain to cover the windows. That is my plan and I think it will work out quite well.
I mean the windows are single pane bus windows they will never be fantastic. My goal is to over compensate in other ways to hopefully counteract them. hope this helps.