Yeah, you should definitely minimize the amount of glass. If you use it with a vocalist, then you should use a cardioid mic and point the null point of the mic toward the glass.
Using glass at the top layer of a gobo is quite common, you see big studios with units like this all the time, and commercially available units like this:
Using glass is only really important when eye contact is needed between performers. It's not acoustically ideal to have glass that close, but if giving them eye contact results in a better performance, then I'll live with it, and use good engineering techniques to minimize the problems the glass imposes.