Glenn will no doubt be along shortly to explain the specifics of SQF's view on this.
There is a specific clause I can see though which appears to indicate your auditor is right. But I do think it's nitpicking.
2.4.3.10 Suggests you need to identify CCPs.
I have to admit with GFSI schemes including things like radiological hazards that they permitted FSMA based food safety plans instead. But looking at the wording of BRCGS it's similar.
From a HACCP perspective however, people will tell you a process PC is the same as a CCP. It's not. Sometimes it's an oPRP and sometimes (certainly if you don't work to ISO22000) even a PRP in "traditional" HACCP due to the way that prerequisites are considered within decision trees. You will have more preventive controls (including more process preventive controls) in a FSMA food safety plan than you'll have CCPs in a HACCP plan.
But does it matter to food safety? No, not at all. The process to get to the end point of control measure that is controlling what would be a significant hazard in the absence of PRP control is just a different tool to get to a similar place. If it was a problem, the US would have vastly worse outputs for food safety related to the way risk is considered. (You don't.)
It is possible and perfectly acceptable to combine a food safety and HACCP plan. In fact I'd really recommend it. Those of us who have been under FDA for export to the US have done that for years. It's only US plants I see doing separate food safety and HACCP plans for audit purposes only.
So I'd recommend just having an extra column and using the Codex decision tree to decide which of your PPCs are CCPs. Far too many Ps and Cs...
