Because he was a decent President?
Though by mistake , he appointed Warren and Brennan that started desegregation. But, at the same time he brought Richard Nixon on and started the Southern Strategy.
His time as Army General made it possible for him to see the evils of separatism and apartheid due to Berlin's and Soviet division among themselves and the Jews.
Having not served as Army General, he would have not been president and done such a thing as start the desegregation, as well as Truman of America.
Actually, Eisenhower was not a big fan of desegregation, at least while in the army. In fact, during a testimony before Senate, he voiced his scepticism toward desegregating armed forces.
As President, he long ignored the issue, despite appointing Justices such as Warren and Brennan, that made desegregation rulings possible. However, at the end, he knew there is no other way and acted accordingly.