Charles Gittens, the first African American Secret Service agent, joined the agency in 1956, during the Eisenhower administration. He protected Presidents Kennedy, Johnson, and Nixon, and in 1971 he became the Special Agent in Charge of the Washington field office.
Abraham Bolden joined the Secret Service in 1959, also during the Eisenhower administration, and in 1961 he became the first African American to be appointed to the White House protection detail.
So, no, the African American agent in "The Impossible Astronaut" wasn't at all unlikely or unrealistic.