So basically you're just attempting to blame everyone but the party who seems to be most responsible based on evidence collected by an intelligence agency (known to have massive resources at their disposal) where calls between ISI officers and militants were intercepted?
I don't know if you noticed, but I had virtually 0 input on those earlier threads mostly because there was no information out there to make any intelligent judgments. But sorry mate, I'm going to have to go with the good folks of the NYT on this one.
The NYT report is based on carefully leaked information by alleged CIA and US admin. sources - this is essentially a US establishment piece.
The 'good folks' in the US media also swallowed the administration POV hook line and sinker when it came to the Iraq war, and the lack of objectivity was pathetic, so lets not try and paint the 'good folks' at the NYT as some sort of messianic harbingers of truth.
My biggest objection to this piece arises from how 'senior government/military figures' are accused of being behind this, not just certain sections of the ISI, which might have been somewhat credulous.
One could argue that the accusation of 'blaming everyone but yourself' can be equally applied to the US in this particular case - where it tries to hide its failures in Afghan development and halting the drug and weapons trade supplying the Taliban by pushing the ISI into the limelight.
As for US motivations, they are clear IMO, and I have made my arguments on this; the US has extremely little leverage with the GoP/military at this point - neither side wants a confrontation nor can they afford one. The CIA is a US agency designed to further US interests - it has overthrown governments (democratic and dictatorships) sponsored violent coups and regimes, and caused a whole lot of bloodshed the world over. No one is arguing the 'massive resources' at the CIA's disposal, but those resources are first and foremost to project the US interest, nothing else.
This is just another means of pressure by the administration.