Shubuta is in the southern part Clarke County, Mississippi. My focus is primarily on Lauderdale County, Clarke's neighbor to the north. I do know that there were several hospitals set up in that (Clarke County) area during the period, so you're certainly on the right track. You might like to check on Kathy Murry's MSGenWeb site for Clarke County. It's at:
She's very knowledgable of the area and genealogy of the area. She'll be glad to help you if she can.
If memory serves, there were quite a few burials at Enterprise Cemetery, near Shubuta and you can find a partial listing of that cemetery and three or four other area cemeteries at:
I'm sorry I couldn't be of more help. I hope you find you ancestor.