I just think you're trying to render the discontinuity between the Christian Theologians and the Greek Platonists/Aristotelians much larger than it is. Christianity asserted itself during its rise as a philosophy, not a cultic religion, as did then-contemporary Judaism. Christianity and Judaism's type of religion, though it now dominates much of the globe, was very unusual. There's not this radical break between Christianity and the western pre-Christian philosophical tradition, there's a continuation of the traditions of the predecessors. Indeed, Christianity embraces much of Roman philosophy's preferred forms of metaphysics (Neo-Platonism) and ethics (essentially Stoic), possibly as early as Paul's writings, certainly soon thereafter.
At any rate, to the point of the thread, I think that empowering the Mu'tazila is probably your best bet on forming a more rationalist, less clerical Islam, but ultimately this is not necessarily helpful. Islam has not "reformed" in the sense of the Western Protestant Reformation because it is a totally different form of religion and has a totally different theory of the state, law, and authority than Western Christianity did. And the reformation brought with it a century of war and some of the most stringent theocratic governments in Western history (Calvin's Geneva, the Puritans). What brought about the enlightenment was not Protestantism, rising education, or rising wealth, but bitterness at the European Wars of Religion and the need for a non-revelatory standard of truth on which to build ideas of the state.