Probably trying to get to India, but a malfunction or problem on the plane caused it to have to request a landing in Pakistan. Pakistan is obligated through international law to assist civil planes if help is urgently needed, regardless of which nation owns the plane, or status of Pakistan's diplomatic relations with said nation. The plane likely headed back to Israel, once the issue was resolved, to get checked properly.
Don't read too much into it.
Besides, Pakistan isn't inherently anti-Israel, but rather it's stance is clear and consistent. Recognize Palestine along the Arab peace plan, and get recognition, along with diplomatic ties.