Under what assumption? PAF jets violated Indian airspace and shot down there 2 jets and blew the hot air out of modis empty threats.Because the probability of success with that is not only low, but also because the international blowback to something like that will be immense. Moreover, there is NO guarantee to your assertion that somehow by eliminating this leadership circle with a 100% success rate(impossible) will not invite some crazy on their end to retaliate with nuclear weapons.
Neither side has the ability to differentiate if a ballistic or cruise warhead is carrying a conventional or nuclear payload. However, India’s early warning is boosted with both their Green Pine systems and additional assets - if they see a few dozen ballistic missiles heading their way; like us they will assume those would be nuclear and will alert their forces to retaliate in kind.
Did India at that time assume the jets were equipped with nukes? It is not as simple as it seems to deploy nukes to forward operating bases, get it through the proper chain of command, equip the nuke warhead to missile/bomb, etc... even the US/Russia do not have nukes on standby ready to launch any second. If this chain of command is disrupted then that will cause even more confusion/delay for the enemy.
Sure India has capable SAM systems/radars but they are not immune to low flying drones/cruise missiles. We have seen time and time again from Irans strikes on KSA to Azeri strikes on Armenia. Russian systems in particular have an issue with tracking objects less than 300M above ground and very susceptible to jamming something which the Israelis take advantage of almost daily in Syria (who has just as advanced systems as India covering much smaller airspace).