Free jazz comes from theory? I don't know. Coleman certainly has some theories (he calls his system of organising musical material "harmolodics"; I know nothing about it, but the blending speaks of a desire to arrive at some sort of urmusic--something that deals with all the musical elements in a more cohesive way, dissolving the traditional hierarchies), but a lot of people say they're bullshit.
It came about naturally, I guess: a number of musicians were interested in bypassing the standard set-up to get to the heart of expressivity and interplay...something like that (consider the socio-political factors involved: the civil rights movement, Black Power, the rise of individualism).
I certainly don't see free jazz as a specifically cerebral music, any more than I see abstract expressionism as a cerebral art.