Actual agents would be incriminated with a real investigation into their activities and collecting solid evidence of their deeds.
Torture has an effect of being able to make just about anyone not only say what you want to make the pain stop, but often psychologically breaks them and makes them actually believe that they did what you tell them they did. (I spent a summer working as an admin at the office of a charity in the UK that rehabilitated torture victims)
The article itself states that it took a lot of time to break these suspects - about as close as you'll ever get to the Pakistani press saying that they were put under prolonged torture.
If you read the whole article (instead of just this line) it talks about their arrest, their possession etc.