Well, there kinda was a period of turmoil following Al-Mutawakkil's assassination, the so-called "Anarchy at Samarra" when the Turkish slave-soldiers and other factions tried to install their own claimants to the throne. The Mamluks also did not attempt to put an infidel on the throne, as all the claimants were Sunni relatives of the deceased caliph.

Also, Al-Mutawakkil, though an effective caliph, was not universally loved. He chopped down the sacred Cypress of Kashmar, infuriating the still numerous Zoroastrians of the realm, and he was extremely harsh on the Shi'ites.

Regarding the Mamluks, at this point in time, many had already converted to Islam, so they couldn't really be considered infidel usurpers. Furthermore, their military excellence was a mainstay of continued Abbasid success, and their dismissal would have weakened the Caliphs' military ambitions, and the mamluks were by and large loyal, excepting cases such as this. Perhaps an appropriate analogy would be drawn between the Mamluks and the Praetorians of Classical Rome; both were highly disciplined military organizations with a penchant for playing kingmaker, though their foreign nature might be a bit more similar to the Varangians of the German Guards of Late Rome.

I suppose what I'm trying to say is that the Mamluk assassination was a purely political maneuver that had no undertones of religious tension, and the sheer usefulness of the Mamluks/ghilmen as an institution prevented their total dissolution.