That's definitely a consideration, hence why I wondered. I could see it going either way. If Victor did, however, that could lead to many interesting story considerations.
Perhaps Victor would be able to see something in Stone's mannerisms that would tip him off as a Rabid Fox -- something only Victor and other higher ups would know. If Victor didn't know him personally, he could have a hunch and go looking through any AFFS databases to try and match -- assuming they even existed still after the Jihad. What Victor decides to say or not say to Stone would be interesting: weighing the political and personal pros and cons of such a conversation. Something a younger Victor would not have done.
To me, that's an interesting personal conflict that I would have liked to see explored. Maybe Stone even tells him after the Jihad and the Republic is on firm ground. Keeping secrets may work in real life, but for a narrative secrets only work if there is payoff somehow.