This is the FBI taking down criminals engaging in a clear criminal activity, and it is silly to implicitly compare it to the NSA fishing for terrorists. All the evidence gathered here will be presented in a court of law, all the techniques used will have to be approved by judges as in accordance with laws and the constitution or the gathered evidence will be thrown out. The suspect and any other future suspects will get a trial if they want. It will be out in the open.
If you are upset that the software you thought was secure and anonymous isn't as secure and anonymous as you thought, that isn't the FBI's fault.