Yes, the cemetery is maintained and is located as part of the property on the Confederate Museum on US 69, though, like you said, I believe the cemetery is within the railroad right of way -- the Katy tracks are just to the east. Not all graves have been identified. As I remember, part of the cemetery was destroyed when the railroad was built.
While I'm obsessing about the site of the Battle of Middle Boggy, I'm not aware of any evidence that casualties of the battle are buried in that cemetery. I believe the fact that there is a cemetery with Confederate soldiers in it led to the assumption that a battle was fought there but the identified graves of the 19th Arkansas were victims of a measles outbreak.
Anytime I hear the killed were "buried on the battlefield" I assume no markers or wooden markers such that evidence of the graves is soon gone.
Having travelled US Hwy 69 through Oklahoma a few million times, I will share with those not familiar with it that not one town (that I can think of) on this highway was a "town" during the Civil War. All the towns grew up when the Katy (MK&T) Railroad was built and the highway parallels the tracks fairly close to the route of the Texas Road (Emmigrants' Road) -- so, Vinita, Afton, Adair, Pryor Creek, Chouteau, Wagoner, Muskogee, Checotah, Eufaula, McAlester, Atoka, and Durant were all railroad stops. Muskogee pre-dates the railroad but became a town after the war.