A political pressure tactic. USA/Nato need Pakistan, its military, and its Intelligence community to overcome their operations in Afghanistan.
Political pressure is always on, often it is just increased to yield bigger results and more "production" for the "investment".
You wouldn't say that if you have watched the Charlie Rose yesterday interviewing ambassador Haqqani and a woman from Pakistan (I tuned in a bit late , so didn't get the names but am guessing he is Haqqani) who he said is part of the government.
The man (Haqqani) said the international community must help Pakistan "clean up"the institutions such as ISI (not exact words, but close)
The woman said the reason kids are sent to madrissas is because that is the only way they can get fed and in the process are corrupted mentally ...
Now, if I understand your point to be that the accusations of ISI and similar are mere pressure tactics, why would these people in the know, use the same tactics?