I get why these bases were originally (probably had a different name prior actually) given confed names, but I don't hate the idea of renaming them now. Ballparks get renamed all the time for somebody currently relevant. Roy Williams court (just the actual court in the Dean Dome), for a local, recent example.
Most of these specific bases were named after confed generals who were supporting the reconstruction and reconciliation by the US, which we know didn't win these revered generals any popularity contests with southerners at the time. There's no shortage of contemporary writings about Lee in this regard.
It seems a small thing to do, and I can see where it would be bothersome to a patriotic af African American soldier stationed there.