The 109th really has no significance here, except that many were sympatizers (not really copperheads), and some, after being captured, decided the rebels had better arms, food, etc. than they had at that time (and perhaps the only time). Grant's order to charge them all (except Co K) with desertion, etc. had more to do with the politics than anything else. If you read most of the files individually, you'll find that many of the 109th (the 200 or so) enlisted individually in other Cavalry or Infantry units.
If a Union soldier stationed at Cairo----Maybe he joined the Navy (they aren't included in the NPS site); maybe he worked as a nurse at the local hospital, or in the shipyards as an employee for the government---there were numerous jobs held by people hired by the government at Cairo then.
I find no trace of him being in the Confederacy either. Had he been a private citizen, arrested for treason, etc. in 1862-63, I doubt that he would have been held at Cairo for a long period of time. The majority of those who were arrested here (private citizens) were made to take the Oath swearing to their loyality & released and watched, or taken to Cinncinnati, or elsewhere (some were taken to N.Y., some to Washington D.C.) if they refused to take the Oath. I've found no reference to a Jonathan Boyd, but will certainly try and keep and eye out for you.
You might try asking Darrel Dexter <darreldexter@hotmail.com> or through the GSSI website. He's compiled several books for Union, Alexander, and Pulaski Counties, most being sold by GSSI. I don't own all of his Union Co. books though, so I can't search for you. Also, Tim Casey who maintains the Union Co. website (genweb), is related to many people buried at that cemetery. He may have some information also.
Years ago there was a lady who "named names" of Southern Illinois copperheads. Her grandfather was a leader of the Sons of Liberty or KGC in Southern Illinois. She apparently waited several years before publishing her book. When it was published, one person bought all the copies to "protect identities". She lived in Union Co. at the time. (I've never seen a copy of this book---just heard about it).
Good Luck!
Ann