It's not that hard to figure out. The writer, if s/he is your professor or TA, is bluntly asked to list the course(s) that they taught you as part of the PharmCAS questionnaire. Coupled this with the transcript, it's easy to connect the letter and grade.
It is a tough choice. I think I would still go with the original writer assuming that it really was because of the final that everyone did bad on. An honest revealing letter with positives and negatives is better than a general neutral one.
I could've sworn that I saw this posted somewhere a while back...🙄