This page has 3 more. Edmund Brooke Alexander (frontier duty through 1863, then provost and recruiting), John J. Abert (head of Topographic Engineers, ret. 9/61), & George H. Thomas (who deserves every honor, but was only a major until he was promoted to replace Lee).

https://www.nps.gov/rich/learn/historyculture/-if-virginia-stands-by-the-old-union-robert-e-lee-resigns-from-the-u-s-army.htm