Unlike so many other Arkansas counties, the Polk County courthouse, as far as I can tell, was not burned down during the war, so they should have relatively complete county court records (unless there was a post-war fire I don't know about). If you go to the GenWeb site for Polk County, there should be a list of resources available at the courthouse, and contact information. I visited a few courthouses many years ago, and found, for example, county court records of home guard appointments from the 1861 period.
As far as Confederate pensions are concerned, civil officers and employees of the Confederate government were eligible, but state, county or local officials were not (unless they provide documentation to prove that they performed some specific service to the Confederate government).