If they're Confederate soldiers they will just plow them under. Problem solved.
Highly unlikely there are any Confederates among these graves. Fort Negley was built primarily by forced labor of black men and women, to defend Nashville from Confederate counter-attack after the city was captured in 1862; some of those laborers are probably those buried there. Nashville in 1864 was the most fortified city in the western hemisphere.
BTW HoustonSam is an unreconstructed son of Confederates and a native of the Nashville area, although not this particular neighborhood. The Army of Tennessee did not move as far north as Fort Negley in its ill-fated 1864 Franklin-Nashville campaign. However I believe there are Confederates from the campaign buried in the adjacent old Nashville City Cemetery, alongside Dick "Baldy" Ewell and the pro-Union Nashvillian Captain William Driver, who gave the US flag its nickname "Old Glory." The number of our dead at Nashville is still not known, but it's a safe bet there were fewer than two weeks earlier at Franklin.
As the remnants of the shattered Army of Tennessee retreated back into northern Alabama behind Forrest's rear guard, they sang of their commanding officer, to the tune of "Yellow Rose of Texas" :
"You may talk about your Beauregard
and sing of General Lee,
but the gallant Hood of Texas
played hell in Tennessee"