Well, neither county's Joseph Abernathy was provably a descendant of Pocahontas nor was that town in Missouri named that in honor of either Abernathy. Those alleged facts are simply long re-told myths that don't stand up to reliable substantiation from extensive genealogical research. Trust me: I've had decades to do exhaustive research on both of those items.
My database on Abernathys is fairly extensive -- growing larger every day -- and for the 1840 US census I have determined the probable identity of all but 6 of the 30 Abernathy heads of family listed on that census, one of whose surname is either mistranslated or misspelled. At least I have researched them well enough to cite them as being on that census and learn more about them. One Joseph is listed as a slave owner with 10 slaves, the other is not. One is aged 60-70, the other aged 30-40.
I believe you need more factual data. The process for you to follow is to start with yourself, write down every 'fact' as a 'clue' about yourself, your parents and their siblings, then play detective: document and verify these clues with official records, including census, birth/death certificates, obits, newspaper articles, and so on. Continue to do this with each prior generation, both male and female, until you can get back to at least the 1850 census. Try not to skip over the documenting process because if you don't do it right in the first place, you will never find time to do it over and your end conclusions will all be suspect. Write or talk to all your aunts, uncles, cousins, and so on. Write down everything they tell you and verify it as best you can. Then you might have a better idea about which was truly your great-great Uncle Joe.
For instance, can you tell me about your parents and grandparents? What were their names, dates of birth/death, location in what census year in Missouri? What were the names of their siblings? Do you have dates/locations for them? Maybe if I had those clues, I could determine which your great-great Uncle Joe was.
Speculation without substantiated facts is very counter-productive when attempting genealogy research and can often lead to incorrect data, cross-linked families and occasionally a truly big mess for someone -- a professional genealogist or dedicated amateur like myself -- to sort out.