While Kevin Flynn remains a protagonist throughout the entire TRON franchise, his program Clu turns HARD in TRON Legacy. The comic book, however, makes it arguable as to whether Clu was ever a Face to begin with.
What's more, Tron himself has traded in his hero status for a badass make over as villainous Rinzler. At least until he snaps out of the Brainwashed and Crazy.
This is not quite applicable, as it becomes very clear that Tron's turn to evil is of the aforementioned Mind Rape/Brainwashed variety. Tron ultimately reverts back to normal by adverting Sam and company to flee while he tries to stop Clu by himself. And he dies in the process.
In Film/Born Innocent. Chris Parker (Linda Blair) a non-crimialized offender, is sent to a reform school after running away from her family. Her brother refused custody of her, and though best Is seen at the end lieing about instigating a riot in the dorm against the house mother when she was refused shampoo.
In Undercover Brother the title character turns his back on the Brotherhood after he falls in lust with Penelope Snow. Luckily Sista Girl brings him back to his senses.
Alec Trevelyan of the James Bond film Golden Eyeseems to be like this during the reveal of him being Janus. But as it turns out, he's been plotting revenge against the British government for the betrayal of his family, who were Lienz Cossacks.
Boromir is a bit of a stretch, though. Yes, he seems to give in to greed when he tries to take the ring from Frodo, but this was more of a momentary lapse in sanity than a full-on Face Heel Turn. Seeing as he dies heroically fighting the Orcs, it appears that he was still an ally of good in the end.
Scrappy from the first live-action Scooby-Doo movie. He went all evil because the gang kicked him out years ago and wanted revenge by taking over the Earth with demons.
In The Wolverine, Ichirō Yashida was apparently a genuinely nice and caring man once, but when his cancer started destroying him, he became obsessed with immortality and turned evil.
In The Incredibles, Buddy Pine's career as Incredi-Boy is short-lived when he is rejected by his idol, Mr. Incredible. But Mr. Incredible learns the hard way that some people are Not Good with Rejection when he goes up against Syndrome, who is actually Buddy all grown up and out for revenge.
Over the course of Mean Girls, the friendly and good-hearted Cady usurps Regina's position and becomes the mean-spirited Alpha Bitch of the school. She goes through a subsequent Heel-Face Turn when she's confronted with her actions.
Also, Jo in the sequel.
Theodora in Oz: The Great and Powerful starts off on the side of Oz, believing him to be the prophesied wizard, but due to the machinations of her sister Evanora, she ends up becoming a Wicked Witch.
Elysia in Warriors of Virtue. Prior to the movie's events, her brother was killed by Yun, which led to her developing a grudge towards him and her turning to Komodo. During the movie, though, she does develop a soft spot for him and thinks of him as a brother. It's this that leads to a near Heel-Face Turn, changing her back to what she was before. Undortunately, her decision to protect Ryan ends in Redemption Equals Death.
Arthur became The Mole for Valentine sometime prior to the film taking place.
After being kicked out of the Kingsmen training program, Charlie and his family join Valentine's plan, being some of the chosen few who will be spared from the upcoming genocide.
Part of the backstory of Mother Malkin in 7th Son. She was a good witch until Master Gregory married another woman, driving her to submit to the forces of darkness and become queen of the evil witches.