This is probably the most telling bit of it:
CLEMENTE: We certainly have ways in national security investigations to find out exactly what was said in that conversation. It's not necessarily something that the FBI is going to want to present in court, but it may help lead the investigation and/or lead to questioning of her. We certainly can find that out.
Basically, this capability exists, can and does get used, BUT the fruits of which aren't directly presented in the courts, because that would divulge too much as to its existence. Instead, it gets used to get the suspect to admit what might otherwise be unattainable through a normal interrogation.
Now the scary part:
This could probably directly provide evidence for not just the Boston Marathon case, but many many other criminal cases in this country right now. For all those other cases though, we risk not convicting a criminal, or worse wrongfully convicting innocent people.
It's kind of sad/scary to think that the FBI effectively has a digital oracle that could provide the information to make many trials look like daytime soap operas.