Anyone know why Eric Millegan of Bones went to jail in Bones yet wasn't written off the show?

I love his character of Zack Addy on Bones and just find it weird that they decided to send him to jail when they didn't write him off the series. I can't find anything about him being busy with other work as I know they do in other television shows like CSI: Las Vegas with William Peterson when he went to do a movie or something. It was a way to explain his absence and yet keep him on the show. What were the writers thinking when sending Zack Addy to jail?