[...] RESPONSE OF TWENTY THOUSAND VOICES Bi-la kaifa. REVEREND MOTHER RAMALLO And now the prophecy... Silence...then a powerful low organ NOTE resounding in the cavernous space. REVEREND MOTHER RAMALLO (CONT'D) He will come...the voice from the outer world, bringing the holy war, the Jihad, which will cleanse the Universe and bring us out of darkness. He will have been born of a Bene Gesserit mother. The Reverend Mother continues speaking of the Prophecy, but we do not hear it. The huge wind organ BLOWS louder and louder, obscuring her voice. The picture FADES. [...]
Yes, the religion in DUNE was a quasi-Islamist religion, but it was not really based in Mohammed just as the Orange Catholic Bible was not strictly Christian.
The Butlerian jihad against the robots that enslaved humanity eventually freed the humans.
The Fremen weren’t supposed to be muslims per se, but every group of people in the Dune books were modeled on existing or historical groups. The planet Arakis and the Fremen are based upon Saudi Arabia, fighting to get control of their own oil (spice) from the British.