Taking out Mecca and Medina will not affect Islam. One of the Pillars is to visit Mecca except to occasion wrath against the Christians and Jews. There do not have to be structures there to visit the spot or crater as it may be. The purest of the Moslems believe the structures to be temptations to veneration of something other than Allah and would tear them down. The Sauds have already demolished the identified house of Mohammed to make way for a hotel for hadjis.That is one of the very few differences in belief between Sunni and Shia. The Shia revere holy places and saints. To the Sunni that is idolatry.
Except that it will - regardless of the taqyyia - many muslims have said that there is no way that allah is the superior and only god if he allows himself to be nuked. (Allah determines everything down to the sub molecular so there is nothing he does not control absolutely).
No muslim will accept the humiliation of praying to 1) a failed god, b) to a radioactive hole in the ground. They have said that if the those places are nuked then they will convert to Christianity, Judaism of atheism.
The Saudis demolish everything and anything connected to Mohammad or came before which might contradict the 5 holy books.
The Shia revere the Kaaba and would take it if they could, but having their allah destroyed, humiliated and shown to be weak will have the same affect regardless of sect.