Stucco and Glass or the most common two components of Southern Architecture. The problem is, they don't like each other, and stucco on glass very often result in scracthed glass. Here is a couple of suggestions to minimize this issue:
Protect the glass and aluminum, or insist that the General Contractor assign that to his crew.
Inspect and maintain the glass protection before and during the stucco process.
Never wipe the glass if wet stucco gets on the glass. It will leave scratches. Leave the wiping for the glass cleaners. They are trained for this.
Wipe stucco blobs off the plastic protective film gently. If you leave a large piece behind on the film, it can be near impossible to get the film off without damage to the glass.
If you do get stucco on glass, spray it with soapy water or WD-40. You want that liquid to get behind the stucco to loosen it before trying to remove it.
If you are responsible to protect the glass, include it in your bid. This is not free to you or anyone else.