Eisenhower was born and graduated West Point in the heyday of that compromise. He also went to West Point, where Lee had studied and been commandant. Like everyone else in the military during his service, he wanted to keep the North and the South together. That was the great rift that politicians and generals had to heal and the effort to do so accounts for Eisenhower's attitude towards Lee, who was not only a great symbol for half the country, but an icon at West Point.
Today, the country, or its leaders, are convinced that we are more divided by race, so they put their efforts into that. In a way, today's military bureaucrats aren't so very different from those of Eisenhower or Pershing's day. The focus is different, but the idea that they are trying to hold the country and the military together persists. They may be right or wrong in what they do, but the same applies to the military leaders of Ike's day.
I point out also, that Eisenhower's mother had been born in Virginia. I don't know how Virginian or how Southern she was, but her Southern background might also have been on Ike's mind when he thought of Lee and the Civil War.
While I agree that in Ike’s youth the country and people’s motivations and perceptions were quite different from now, and that Ike had his own particular background, the question remains: what about that quote from Ike about Lee and his character is incorrect? Yes, Lee was an imperfect man who sometimes made bad choices (just like every other human being who ever lived), he also did quite a number of things right…and that was, IMHO, what Ike was discussing.