If your monitoring of the customer's activity won't be hampered by the lack of CTR filings (some banks use actual CTR filings as part of their monitoring process), I don't see any reason not to exempt the business, assuming it qualifies. You probably could have exempted the customer even while still filing CTRs, even though it seems to be a contradiction.
Just make sure you keep an eye on the customer to ensure it doesn't have a relapse and revert to structuring, real or apparent.
_________________________
John S. Burnett
BankersOnline.com
Fighting for Compliance since 1976
Bankers' Threads User #8