There's a world of difference between what Github did, and the hypothetical where AWS chose a proprietary protocol to access a filesystem. For AWS, as long as the underlying filesystem was "more or less POSIX", the access mechanism is largely irrelevant to lock-in; it would be as easy to switch from AWS as it would be to move between filesystems.
Git was not designed for large files. But what github released yesterday primarily serves to promote github's central-server model for git. Moreover, it seems that it could have been better done within the git protocol itself (modify git to do more sparse pulls, and then try to fetch on a checkout when it is missing blobs, rather than erroring immediately).
I suspect AWS chose to use NFS for expedience, the net effect is positive, but I don't think it would have much mattered anyway.
Github is trying to inject their own server-model into the git protocol, with an extension that is only half thought through; that is a huge step backwards, open-source or not.