Religions are no constants. They have always interacted with each other and with society and are rather flexible. Consider Mormonism, which started as a syncretism of Christianity and freemasonry. In less than two centuries, it changed major tenets like polygamy, racism, etc. because they were not practically compatible with society. Older religions are not immune to this either, just compare modern Protestantism with the Catholicism of the Middle Ages.
Now, Dune happens ten thousand years into the future. It is only to be expected that religions will fundamentally change and merge in such a long time. Which religions will take part in these processes with what outcome is impossible to predict; so Herbert’s guess is as good as any.