You can't get visa on arrival at Ben Gurion airport. See a Timatic search at the Emirates site:
Visa
Visa required.
Visa Issuance:
Passengers with a confirmation issued by the Israeli Ministry of Interior can obtain a visa on arrival if they travel in a group of 10 or more.
Warning:
Visitors not holding return/onward tickets could be refused entry.
Unfortunately, it seems like Israeli visas are stamped on your passport, so it will prevent you from entering some (not all) Arab and Muslim countries, notably Iran.
You could try to get two passports, I don't know if India allows it. You can "lose" the passport with the Israeli visa.
I won't be surprised if there's a better solution, similar to stamping on a separate paper on entry. I didn't find one.