Every long running series that is considered to have "good" lore has gone under countless revisions.
Lore constantly updates itself to make the universe more dynamic, and fun to experience. Indeed, only games with bad lore remain the same, as they refuse to accept that some decisions in past games were terribly dull, or simply just crap.
Much like the change of Cyrodiil from a tropical jungle with no cities beyond the Imperial city, which was a fairly dumb idea in the long run, to what we got in Oblivion, things change constantly to make more sense, or offer more dynamic gameplay.
The change of ghouls was done to make the different types more distinct, and offer new gameplay options for each.
These changes, no matter how much they happen, do not make any past game non-canon, as the main story and side quests still remain, all it does is change completely pointless visual appearances, which change every game anyways, and changes how things are dont mechanically in each game, which changes every game anyways also.
And this isn't even taking into account that people like Tim Cain and Chris A, the people who made the old games, do feel like it fits lore. So obviously they do feel like ghouls were always this way, despite what may have been shown in the game itself at the time.