Last year, I bought an Otterbox Defender for my iPhone 5 purely to protect it when I went on holiday for 2 weeks. My 5 had (and still has) an original SGP Glass T.R glass screen shield (not the current slim designs but one of the original thick designs) installed and I was also worried that the Defender would not fit.
When I received the case , my worries were indeed confirmed as the Defender would not fit over the glass screen shield (the plastic parts of the case would physically fit over the phone and the screen shield however, due to the thickness of the glass screen shield, the clasps on the Defender would not stretch enough to close together so the case did not fit properly).
However, as I bought this over the web and had no intentions of sending it back, I took a screwdriver and very gently applied pressure to the clasps, on every side of the Defender (I think there is one on each side, 2 at the top and 2 at the bottom) so that I stretched the plastic a little. I had to be careful as if I applied too much pressure, obviously the clasps would snap and render the case useless!
I basically kept doing this until I managed to get the Defender to fit and close over my iPhone 5 with the glass screen shield - which it did. This does produce a gap, however, where the top plastic case meets the bottom plastic case (obviously due to the stretched clasps) but when you then apply the rubber portion of the case, it covers up the gap so you can't actually see it.