I've been doing a lot of reading for US legislation recently and what I'm about to share might not be accurate, sometimes it's ridiculously prescriptive. But if you go back to international HACCP standards, i.e. Codex, then sanitation is absolutely a prerequisite, albeit for US plants you would probably mush it together with the US legislation on preventive controls and call it a preventive control (but not a CCP).
I would also argue your RTE area in itself and the controls on ingress and egress of that area are part of your pathogen control for it so if you start mandating sanitation as a CCP there's a bit of "where will it stop?"
If you want a reference though, the first question in the Codex Decision tree is: "Can the significant hazard be controlled to an acceptable level at this step by prerequisite programs?" So how is your FDA auditor claiming that answer is not true?
But I am going to bang the drum a little for FSMA here and preventive controls. I do think a combination of HACCP and HARPC/FSMA approaches is valid. And in this case, I think sanitation is a perfect example. So preventive controls need to have monitoring (normally your cleaning records and perhaps independent inspection by a supervisor?) Validation (you should validate sanitation to ensure it's capable of reducing soil and bacterial presence to a safe level and removing allergens if relevant.) You verify it (you do hygiene audits, swabbing, ideally you'd also track man hours on cleaning.) Ideally you should do all that for prerequisites controlling significant hazards but outside of the US I'd say that practice is a little patchy from sites I've audited.
So I suppose my question is have you recorded all of that (whether you've called it a prerequisite or preventive control) and they're just hung up on terminology or have you got a gap in terms of how you validate and verify that as a prerequisite or preventive control? If it's the latter, I agree with your auditor. If it's semantics, s/he can bore off as they control you'd have in place is the same.