Negation: Javi goes through this after Charon brought him back from the dead and convinced him that his conquest of the Negation-verse and his pending invasion of the main CrossGen universe was a good and necessary thing. Javi, a religious man who had questioned his faith even before his abduction to the Negation-verse, came to look upon Charon as a god, one in whom he could place his whole trust in, without question. He becomes a Knight Templar as a result.
In Sonic the Comic, Nack the Weasel is introduced as a member of the heroic Chaotix — but by the end of their introductory story he's sold them out to the Brotherhood of Metallix, an army of spectacularly evil robotic copies of Sonic. Admittedly a loose example, as a) he'd clearly already turned before the story started and b) the character was always a villain in the Sonic games, so seeing him as a hero first is the unexpected bit.
In Sonic the Hedgehog (Archie Comics), the most notable thus far was Fiona, who turned against the Freedom Fighters in #172 and joined Anti-Sonic/Scourge in Moebius (formerly Anti-Mobius).
Espio turned against the Freedom Fighters and Chaotix to join the Iron Dominion, but returned. It turned out to be a ruse, but it wasn't exactly a harmless one.
And before either of those two... Drago Wolf and Sleuth Dog.
#178-179, though it could just be a political debate in which both sides use violence instead of words.
Geoffrey St. John appeared to have one in issues 219-220, but this is actually a subversion, as it was soon after retconed that he'd actually been working for Ixis Naugus since before either of them were even introduced, making him The Mole instead.
While alluded to in Sonic Universe's Fractured Mirror Arc, the dual prologue/epilogue Dark Mobius - Knuckles' Descent, hosted on Archie Comics' blog, makes it clear that Dark Morbius' version of Knuckles had devolved into a political extremist responsible for murdering Dr. Robotnik. His transformation into Enerjak is depicted as completely willing here, drawing a deliberate contrast to Knuckles' unwilling corruption into Enerjak in the Enerjak: Reborn Arc.
Wizards of Mickey: More like Brainwashed and Crazy, granted, but this happens to Mickey, of all people, in The Dark Age. The incredible burden of becoming the Supreme Sorcerer slowly turns him reclusive and paranoid, which the Phantom Blot takes advantage of to turn him against his friends and into a tyrannical king. Word of God is that they made him evil for the hell of it, although the process is reversed by the end of the series.
