While I do understand the need to properly identify the aforementioned cemetary, I am afraid that our state's budget cuts severely hinder any investigations at this time. Your best bet would be to contact the closest university and see if they are interested in the project. Universities act under the strict guidelines of Louisiana's Division of Archaeology and often can obtain funding that is not currently available on the state level. They generally connect these projects with a field school for their students. Another possibility of a 'host' for the project, although more of a stretch, would be the Smithsonian Institution. I worked with them in their examination of graves near Port Hudson back in the late 1980s. The most interesting find of that program was what was determined to be the grave of a Union and Confederate soldier buried together. They were reburied together in a ceremony on the state park grounds.

As to the plans about a Confederate memorial, the locals I know or have spoken with say that the graves in this particular cemetary near Camp Pratt belong to Union prisoners held there not to Confederate soldiers. I believe any Confederate soldiers would be buried in town, probably near the other hospital you mentioned. But again, the records are not very clear.
I hope this helps.