Yes it is a civilian nuclear deal, and yes currently there are only two reactors used for generating electricity (with the third expected to start by next year) - that is why Pakistan is looking to construct more NPP's to generate electricity - how do you propose Pakistan have more than '2 reactors used for power generation' without such sales?
Secondly, the two reactors under IAEA safeguards were put there willingly, since Pakistan has a separate military nuclear program.
Because Pakistan is producing both Enriched Uranium and Plutonium and that also with a very good speed. That's why your weapon arsenal is increasing. And its not possible with just 2 Nuclear reactors.