1. Try an adhesive film attach on your sample film and lift off.. adhesive films commercially available called OCA (optically clear adhesive) from 20 um thickness. So finally you can have your film on OCA film. Optical point of view, this works good.
2. Try the Teflon substrate instead of Sio2, Teflon (Polytetrafluoroethylene (PTFE)) have low surface energy compare to Sio2 and easy to lift off or detach.
It is just an idea, but have you tried ultrasound? The Si crystal is much stiffer than the protein film. So, at the proper frequency it should oscillate much stronger and the film will detach. But it is just an idea.