Eisenhower wasn't the first president who had to issue an executive order to achieve racial integration against the wishes of many of the rank-and-file. Franklin Delano Roosevelt had to do it in 1941.

When African American men volunteered or were drafted for military service, they served in segregated units and were often shut out of combat positions, instead given jobs like cooks or gravediggers. The military and defense industry operated under the same Jim Crow attitudes that Blacks suffered through in the South.

After the U.S. entered the war, activists and journalists pressured FDR to make good on the promises of his famous Four Freedoms Speech and apply those freedoms to all Americans. After a lot of resistance on his part, the President issued Executive Order 8802 on June 25, 1941. It prohibited discrimination by race in all national defense industries:

Whereas it is the policy of the United States to encourage full participation in the national defense program by all citizens of the United States, regardless of race, creed, color, or national origin, in the firm belief that the democratic way of life within the Nation can be defended successfully only with the help and support of all groups within its borders;

Further:
Now, Therefore, by virtue of the authority vested in me by the Constitution and the statutes, and as a prerequisite to the successful conduct of our national defense production effort, I do hereby reaffirm the policy of the United States that there shall be no discrimination in the employment of workers in defense industries or government because of race, creed, color, or national origin, and I do hereby declare that it is the duty of employers and of labor organizations, in furtherance of said policy and of this Order, to provide for the full and equitable participation of all workers in defense industries, without discrimination because of race, creed, color, or national origin... (Source)

This order just applied to defense industries, not to the service branches themselves. It would take another president, and another Executive Order, to do that.