Because it shattered the audience's collective suspension of disbelief. Having watched secondary character grow, change, develop into a 'matured' version of themselves is part of the reason people care about characters in fiction at all. Even comedies. This episode basically threw all that for Skinner away. Even though it doesn't affect later plots it's still presented as something that happened. People don't forget that it wasn't presented as a horror story read by an ax murderer, or a fantasy interpretation about a puppetshow Bart put on for the Retirement Castle as community service for some kind of vandalism.
It wouldn't be an exaggeration to say Skinner was in the top 7 favorite characters on the show at the time. Maybe with Burns, Flanders, and Krabapple from the supporting cast ahead of him. But now the things that made up such a huge part of his character are lies. Which don't jive with his now revealed real identity at all.
I don't know how to explain it better than "It only matters if you cared to begin with"