Yes, happened to Chris Perez last year:
http://espn.go.com/mlb/story/_/id/9629657/chris-perez-cleveland-indians-closer-guilty-marijuana-case
"Under the drug agreement between Major League Baseball and its players' association, marijuana offenses generally result with the player undergoing a treatment program rather than discipline.
Perez is participating in the treatment program and is subject to regular drug tests, defense attorney Terry Gilbert told The (Cleveland) Plain Dealer."