People are routinely monitored, officially and unofficially by all sorts of recording devices, CCTV, phone records, CVFDRs, car trackers fitted by insurance companies to reduce premiums, in car video recorders, etc., etc.
It has long been a principle of British law that all evidence must be presented before a Court whether or not it might be predjudicial or beneficial to a defendant. It is for the judge presiding to rule whether evidence is admissible in considering a verdict.
The fact that evidence of any sort was recorded for purposes other than for consideration of a legal case is irrelevant. If evidence exists in any form, it should be submitted before a Court if that is what is required to reach a fair and considered verdict.
If you were the victim of some crime, you would be very upset if clear CCTV footage of the offence taking place was disallowed because it was recorded through the front window of private premises, or it was recorded by a traffic camera and therefore not for the purpose that the system was intended.
FDCVR's are intended to identify the causes of aircraft accidents. That should not preclude their use where appropriate to accurately establish the facts and where blame might lie after the safety investigations are concluded.
People in all walks of life and careers are routinely monitored and disciplined if wrongdoing is discovered. Pilots have no right to expect to be exceptions to the rule.