You can be charged on suspicion of a crime even if you are not guilty of the crime. Larceny (in general) is taking an item with the intent to permanently deprive the owner of it. Larceny is a specific intent crime, and requires that you specifically had criminal intent at the time of the incident. Assuming you were knowingly taking an unauthorized discount, you could be convicted of larceny in most States. If you thought you were taking an authorized discount, you could not be convicted of larceny. The problem is what the trier of fact would believe.
A "steep" discount? From someplace that doesn't really discount?
There is a serious question as to whether you possibly could have believed him when he said he was "authorized" to make those discounts.