Two things:
1-That ending isn't canonical
2-Johnson isn't actually a particular character in Halo 1. The name is mentioned in the credits, but "his" in-game appearances are no different than those of the other stock marines. Any appearances of the black sarge in Halo 1 that can be considered to be Johnson are those that were canonized in later material. But it's worth noting that some people at Bungie itself didn't want to mess with "Dust and Echoes" as far as the games are concerned, which is why Johnson's introduction to the games in Halo 2 lampshades his escape rather than explaining it.