When you say non-compliance for non-heat treated pallets, what standard is that held against? I find nothing in 21 CFR 111 requiring heat treated pallets.
Beyond that, if the concern is pests infecting an untreated pallet, there's no guarantee that a heat treated pallet wasn't subject to infestation after it's treatment. Our facility uses a trailer inspection form on received material. This helps us to prove we are monitoring things prior to allowing them into the facility, and ties into pest control too. I think something like that along with a visual inspection of pallets during your pest control checks could be sufficient (even if an auditor doesn't think it's ideal).