I think the following might work. Imn my case, I used the nodeaccess module to set access permissions for specific nodes, then set it so the role I chose could only view specific nodes. Then, the nodes that are not allowed don't show up in the navigation menu. I did this to hide an entire main item in the primary menu, so am not sure it will will with individual sub-menu items, but suspect it will. 

Good luck, 

Bill