The civil ties may be terrible now (mostly because of Obama's insistence on being pro-India and anti-Pakistan), but military ties have always remained strong. Even during times of crises, PA and USAA have always remained in touch, and have largely ignored concerns from civilian leaders. That's not to say that the PA and USAA trust each other; indeed, the Abottabad incident, along with the killing of 24 PA soldiers, and the Raymond Davis incident have made each side wary of the other, but they remain committed to cooperate, despite what the civilian leadership is led to believe.
If Obama was to cut off all contact with Pakistan, and get rid of diplomatic relations, the USAA would still continue it's relationship with PA, at least in secret.