Actually, yes, we are. That’s a good thing, in philosophy.
As to Lee, I don’t know enough details especially of political machinations with the CSA and the military.
This makes it sound as if Lee did nothing to debate with his civilian authority.
Could it be he tried to honor the republican principle that the civil must rule the mil? Did he try to out-Washington Washington?
Washington had much the same approach, up until Valley Forge. Tired of the waffling and incommunication and corruption including people scheming to get rid of him and Arnold, E.g., Washington essentially said “no more” with constant letters to Congress and requests. He took more command than he had and things went better. Washington acted always judiciously and wished to be as republican as possible and not show tendencies to have military dictate everything. But he found the line was too close to civil so moved it a bit. Same principle when he pushed for stronger mil as many were scared to death to have too much mil power “standing” and so forth.
Maybe Lee wanted to carry forward the idea that mil must be subordinate to the civilian, but did not move that line a tiny bit to do better?