Kittyhawk of Sparkling Generation Valkyrie Yuuki fame started out with a fairly popular webcomic called The Jar. Sometime around when she was having problems with her domain because of traffic, she took the whole website down. During the downtime between it and SGVY, she came to really, really hate The Jar and absolutely refused to put the archives back up. This seems to have faded recently due to her now selling it on CD format.
In-story example: Justin in Punch an' Pie submitted an absurd story about a bat with a gun to a publisher. They published it. People ate it up. Now he's one of the most popular writers around, and he's sorry he ever wrote that story.
Before Ben "Yahtzee" Croshaw gained fame as a video game critic, he wrote several webcomics. In his words, they "came out of a dark time in his life from which he has determinedly moved on without a backward glance." Moreover, just to make sure no-one would be fooled into thinking he cares about his old works, he has gone on to officially disown them, including every webcomic he ever made, every game made before The Trials of Odysseys Kent and every work of fiction he has written before the age of twenty, encouraging his readers to dispose of them in the nearest possible natural disaster should they ever get their hands on his old work. Makes sense, given his utter hatred of most gaming webcomics, especially Ctrl+Alt+Del.
This is the rule, not the exception, for virtually any Matt Wilson production (namely, High Score and its animated spin-off Bonus Stage) to date.
A humorous parody happens in an issue of Mac Hall. During a con recap in which about twenty webcomic artists are on stage at once, the others give non sequitur-esque answers (Sluggy Freelance was my grandma's nickname), Ian simply holds up a sign that has "YOUR MOM" on it.
Josh Lesnick seems to feel this way about his older webcomic Wendy, seeing as he's just recently taken the whole thing offline since it's already been there long enough in his opinion. The characters themselves, however, continue to live on in comics such as Girly and whatever22.
The main reason RPG World ended prematurely when it was on the verge of finishing. Creator Ian J. came to resent the direction he had taken the comic and in the end just flat out abandoned it. He did offer anyone interested to come finish it, but when the fans voiced their opinion, he told them to "F** K OFF!" and retracted the offer. The series was left without an ending until it reappeared in an episode of OK K.O.! Let's Be Heroes, wrapping it up for good.
Rick Fortner and Rebecca Burg hate the original Job Hunting, the second story in their A Loonatic's Tale series. The final form was hastily edited with unfortunaterestrictions on the amount of weapons and violence (ie there couldn't be any) in order to make it fit a school assignment. They're currently drawing a remake, Rehired, which is the canon version. They use the original version as a barometer of peoples' ability to detect quality and/or speak frankly; anyone who says they liked the original Job Hunting lacks the capacity to offer meaningful criticism.
Bittersweet Candy Bowl: The author got rather fed up at the unsettling number of fan characters in the community and the amount of focus they got. The cast slowly decreased in number over the years.
"Better Days was created when I was a very different person. I had very different views, values, and priorities, and I evolved as a person as I was doing Better Days over the course of six years. There's a lot in Better Days that I wouldn't include if I was doing it today. There's a lot of things that I wrote that I wouldn't have written that way, now. I don't like looking at the old pages. I don't like looking at the old art. It's embarrassing and bad in my eyes. I don't like lingering on the past. It's enough that I've left the archive in place, and find myself having to explain some of the themes and events depicted in Better Days, by a much younger, less mature creator, compared to who I am today."
It is no secret that Tim Buckley ultimately came to utterly despise the characters of Scott the Linux guy and his pet penguin, Ted. Not only has he effectively written them out of the comic, he's gone to increasingly severe lengths to ensure no one knows who they were or even remembers that they even existed, up to and including banning anyone who says that they do remember them or even mentions them in any way.
Word of God claims it's less despising Scott and more the fact that he was a one-note character that Buckley didn't know what to do with, beyond Linux jokes and his final The Reveal storyline.
James Kochalka discusses it with his son in one American Elf comic page.
Shin-Goji has been slowly purging his website of connections to the K-Girls, which he initially introduced during a "darker period" of his life (before meeting his wife) as an attempt to boost traffic to his comic, culminating in his recent announcement of completely deleting all of their galleries from his server in favor of focusing on his own artistic efforts. Considering that almost all of the girls' creators had long disavowed them as Old Shame as well, this is not entirely surprising.
KC Green has expressed large dislike in recent years for his earlier webcomic Horribleville and his short-lived series Literally All I Do All Day. He says he made them at a time where he felt too negative about life. He also recently tweeted "i have one last copy of horrible ville and i want to set it on fire".
Michael Shelfer, the artist for Vampire Cheerleaders since vol.3, admitted he didn't like Heather's character, by saying he thought she was "one-dimensional" and said he didn't even like drawing her. Which was the main reason she was written out near the beginning of volume 4.
David Willis has grown to really dislike his original webcomic Roomies!, sometimes the art, but mostly how much of a different person he is from then. Instead of distancing himself from it, he has chosen to republish it daily, often gleefully pointing out in the author's commentary how terrible certain elements are. At the very least it's a positive example though.
Hiimdaisy has long retired from making video game comics and feels that the memes surrounding them have become tired out. In response to an unofficial Kickstarter campaign for an unofficial continuation of her comics:
"i made a vague tweet about it last night, so here is a clearer one: there's a KS campaign attempting to raise money to continue hiimdaisy"  "i have no connection to it and i absolutely do not endorse it"  "yes, it was me. i wrote those old comics and i have been tired of them for 4 years. i also killed mufasa, etc."  "why would anybody want to be known as "the person who created that meme"