That would not end Jihad or even damage it terribly. The hard core to which all other moslems defer, believes that shrines, even the Ka’aba, are idolatrous. The structures of mecca are retained as moneymakers- producers of some of the resources necessary for Jihad. Wahhabi the fundamentalest of the fundamentalists call for its destruction along with tombs and other shrines. The necessity for every moslem to perform haj- pilgrimage to Mecca- doesn’t require structures, only a place. The early house of Mohammed in Mecca has recently been replaced by a hotel for pilgrims. Destruction of mecca by non Moslems would merely provide a rallying cry and loud propaganda for Jihad. Nuking Mecca is not a substantial threat.
If what you say is true, then there is NO end to Islam. The only other alternative (if Islam can’t be destroyed by nuking Mecca, as you say) is killing every muslim on Earth- an impossibility, as there are over a billion of them.