It could be worse, the user has the old rsa host key present alongside newer ed / ecdsa keys, they may never rotate out the rsa one. A future mitm simply only advertises the rsa key, and mitm passes.
Users will need to actively remove the old rsa key in order to be safe. It's my first question, and a colleague suggested that they believe that the private key was not seen, however, I don't see that in the post - unless I'm missing it - and I really want this stated very clearly somewhere.
I tested this and on a new enough OpenSSH client, the RSA key gets replaced using the mechanism described here: https://lwn.net/Articles/637156/ (if you connect using a key other than RSA).
To be honest, I'd expect something like this to be mentioned in the announcement.
It's not about the certs. To execute a man-in-the-middle attack the attacker has to literally put themselves in the middle of the route your packet takes to get to github's servers and intercept it.