I'm also working on an Illinois/Inoka civ...
From wikipedia:
It is currently unknown whether the Illinois Confederation peoples, including the Cahokia, have any relationship to the earlier native builders of the mounds civilization.
The Cahokia (tribe) are different from Cahokia (city), which was simply named after them. Both civs could easily coexist alongside each other since the Illinois come from a much later time period than the Mississippians. And yes, you could technically make one civ out of them, but I think it makes much more sense (both historically and design-wise) to keep them separate.