Well, the collaborators would have much more experience in governing...
Depending on how dire the organizational needs of Bajor were at the beginning of independence, the only practical choice might well be to beg for the collaborators to keep up the good work, since the heroes of resistance would realize none of them
knew how to keep food flowing to those in need.
Certainly we never learned of any wholesale slaughter of collaborators once the Cardassians fled. Some of the collaborators slithered into the woodwork, some were declared non grata in absentia ad hoc, but stories of open, violent deposing are missing.
Perhaps significantly, we never quite learned whether the provisional government differed from what Bajor had before the occupation or not. But we heard of no changes in government in "Accession" when Akorem Laan made Bajor return to the old ways for a brief while. It would make sense, then, that the provisional government would be quickly erected using the time-honed traditions of the caste society. In such a case, a resistance strongman might have a say on which born-to-lead politician got which seat in the new government, but he would have no real chance of sitting there himself.