Original Anon -
In your post you said "the customer was in a hurry and didn't want to take the extra time needed to complete a CTR." I don't know if you meant this literally.
I have never considered it a good idea to allow a customer to complete the form. If the account was opened properly, your bank more than likely had all the information needed to prepare the form after the customer left.
Regarding your question - the bank has a responsibility to file an SAR when a customer inquires about the reporting threshold and then deposits less than $10,000. I know it seems "defensive," but there is no way to get around it now that you have knowledge of the situation. File and be safe!