You can assist in the capacity of the Americans with Disability act, but you cannot do anything to sway his answer in one way or another, if you read him one of the questions and he does not understand, then you should ask for clarification from the person behind the counter in which he/she is suppose to explain what the question is trying to determine. When I sell a gun and someone has a question, I always explain what it is asking so they can answer the question as it pertains to themselves. If you both have CCW, I don't quite understand what the clerk had a problem with?
There are no legal penalties for reading a form to another who has difficulty in their sight, but they need to confirm they understand what is being read to him so that they can answer for themself.
The American with Disabilities act requires that anybody asking for assistance, be provided assistance in completing government forms so that they can understand the statement/question and then answer in a clear and concise manner that pertains to them and them only. Difficulty in sight is not a reason for denial and requiring assistance in filling out a form is not a reason for denial, Being blind does not disqualify you from purchasing a gun as long as you meet all the requirements of the government background check.
Now a FFL can refuse sale for most any reason at all, but it sounds like the counter person in this case has not been informed correctly by his upper management of how to properly handle a legal transaction of this nature.
The clerk needs more training.