No, they can unlock it, copy the data and give it to the FBI. No harm to precious Apple and their product security. They could actually perform the operation with an FBI representative present but with no knowledge of how the data access is performed.
Defense lawyer's dream: some shmuck runs unknown SW to gather evidence about a suspect with a completely clueless LEO watching. Judge: the evidence is inadmissable, the conviction is vacated.
If you are suggesting the phone contents could aid further investigations that is different. But that data can be gathered other ways. Start with all the people who ever went to his mosque.