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NASA has explored inflatable modules; they used a series of outer layers to reduce the energy of the debris, plus an inner layer made out of Kevlar.

http://spaceflight.nasa.gov/history/station/transhab/

The layers would have to be transparent, which greatly increases the difficulty of the challenge. Unless, of course, the plants were grown using artificial light rather than natural light. In that case you wouldn't need a greenhouse at all, but instead a wall of solar panels to power the added utility demand.

In the Ben Bova Mars series they have strategically positioned piles of patches that get sucked up and stuck in the holes. Maybe you could accomplish something similar with a middle layer that was oversized and stuffed in between the outer edges...