At our airline FDM is being used for several years now, and we do get regular information on the analysis of the data.
There are several (I think about 3-4) security measures in place to keep the data anonimous, e.g. flight numbers are not stored.
As for your question
I don't know about the laws and jurisdiction where you are living/working, but where I live, it is illegal to use such data against the employee. Any labour court would dismiss any claim by the airline in such a case.
Besides, using information gained by FDM for disciplinary measures would be plain counterproductive to any 'non-punitive' reporting system, which many airlines use.
Just my two cents.