TL;DR pretty sure it's not touching git source at all.
Looking though the GVFS readme: https://github.com/Microsoft/GVFS it appears that it actually wraps git, which would make sense because in that case they would have to explicitly add support to each git host and provide individual platform ports of GVFS (all of which would be unnecessary if it was actually upstreamed into git).
So that's good... git is one of my favourite open source tools and I would really hate for M$ to start polluting it. I don't care if GVFS is a good idea or not I just don't trust the fuckers and they will always deserve that suspicion.