I would like to know when and how exactly Israel "helped" Pakistan? Are you talking about the time they sent aircrew to India to assist in a particular air operation or when they had aircraft ready to strike Pakistan's nuclear facilities from Indian soil? I'm not sure if I would classify all that as "helping" Pakistan.
On the other hand, if you are talking about the component they supply lockheed martin for the F-16 Block 52s, then you should understand that they are contractually bound to supply the said part(s) for Block 52s, regardless of which country is the customer for Lockheed. If Iran would have bought those Block 52s instead, the Israelis would have had to supply parts for the Iranians as well.