The 19-year-old star's role as Jake Harper was thrown into doubt when he branded the series "filth" in a Forerunner Christian Church video testimony, which went viral when it appeared online.
The show's executive producer and creator Chuck Lorre now reveals he spoke with Jones about the comments, and insists the teen is still part of the Two and a Half Men family.
Jones has enjoyed less screen time in the current 10th season due to his character joining the Army, but he will be back on set next week (begs14Jan13) to shoot more episodes.
Lorre tells USA Today, "He's coming back next week. He's part of our show. He's part of our family. We love him.
"I was concerned about him continuing with us, but he's entitled to his journey. He's a sweetheart. He's fine. He's 19, man. Cut him some slack. He is a beloved member of the cast. He has been a great, great young man for 10 years."
In his first episode back, Jake will get a new girlfriend, to be played by My Name Is Earl star Jaime Pressly.
Joking about Jones' remarks, Lorre added, "The show's kind of filthy. We work hard. We hope it's funny, as well... The episode we're (shooting) next week introduces his new girlfriend, an older woman with three kids, a tattoo artist, played by Jaime Pressly."
Jones expressed regret soon after the controversy, writing in a statement, "I apologise if my remarks reflect me showing indifference to and disrespect of my colleagues and a lack of appreciation of the extraordinary opportunity of which I have been blessed. I never intended that."