Simple... If I were Bush, faced with this, I'd conference with the General at Whiteman AFB (where the B2s are), SecDef, the general in charge at NORAD, and the JCS, go over the MAOs (major attack options) with Mecca and Medina as the primary targets aiming for the Grand Mosque in Mecca and the holy sites in Medina, use the low yield (250KT, no megaton bombs--has vaporize/incinerate effect but less long term implications) on the B2, the one that is launched via an air/ground cruise missle, order a sorty of those planes to bomb those sites, while particularly avoiding attacks on the surrounding areas.. Also would launch F14s from carriers in the Med to level the Al Aqsa Mosque and the Dome of the Rock)...
If theory is corrct that destruction of the grand mosque and kaaba in Mecca would put an end to Islam, then no more need be done, other than wipe out the remaining individuals behind terror attacks and outlaw Islam.