Again this pertains only to security aid … this has got no bearing on the civilian aid. Worst case scenario … if Pakistan feels US is asking for soemthing that it wont comply … just refuse … all that is going to happen is, the “military” aid will be stopped. “Lekin yahin to mushkil hai” … come on would Pakistan army want that to happen … while rest of Pakistan is getting the benefits of US aid they will loose out on it … you see only THEIR is connected to this bill 
The said clause for you in detail … again nothig that Pakistan has not already pledged to international community
(1) the Government of Pakistan is continuing to cooperate with the United States in efforts to dismantle supplier networks relating to the acquisition of nuclear weapons-related materials, such as providing relevant information from or direct access to Pakistani nationals associated with such networks;
And it is not Limitation of “certain assistance” … it is limitation of "Security " assisstance