Geckos are VERY good at cleaning their toes. I would imagine merely offering it a small cup of very shallow water down at the ground level would give it the tools it needs to clean its own foot and climb the glass, all without any added stress.

I recently went to a gecko exhibit at the Museum of Science in Boston. There was a cool video explaining how their toe pads work and it also addressed the issue of their toes getting dirty. They know how to get them clean again. They're very delicate. I'd be EXTREMELY careful doing any kind of active manipulation of their feet or toes.