Was this at the Lafayette store? The manager there is very pro-gun, however is a newer manager and new to being on the selling side of firearms. It doesn't surprise me that he didn't know the ATF rules and was just going by what he'd likely been told. Good for him that he stepped up to find out the what the rules really are.
As of today (14 Feb 13), this policy has not changed in practice. I had to give a phone number to complete my purchase of a Ruger SR22 this afternoon at the Lafayette store.