Peggy winds up with Steve courtesy of Avengers: Endgame, the extent of Hydra’s infiltration isn’t revealed on a large scale until Captain America: The Winter Soldier, and Coulson probably would have known if there was anything in the S.H.I.E.L.D. history books about the legendary Agent Sousa living to tell the tale of what happened at Area 51.
Does Sousa Have To Die?
Nothing points toward him absolutely having to survive for the timeline.
“Alien Commies from the Future” revealed some key details about Sousa: he and Peggy Carter apparently weren’t in regular contact, he had suspicions about Hydra infiltration in S.H.I.E.L.D. that were serious enough that he reached out to the CIA, and he might have already seen too much for him to have a long future.