Is there a way to simply use ffmpeg for this step (if it has been built with –enable-avisynth)? It seems like all Hybrid does is use a simple(?) AVISynth script.
Can you export the AVISynth script you use from Hybrid and post it here?
A quick search also brought up github.com/hclivess/videer, which seems like a simpler deinterlace tool that also uses QTGMC.