I haven't read the entire Mitchell Report.. I basically just skimmed it looking at the names implicated. Have you read it verbatim? I doubt it.. cause it's freakin 400 pages long. So I can't confirm or deny if there was any new info on Bonds in it. But that isn't even relevant.
Anyway, the indictment is because they think Barry Bonds lied to the Grand Jury. In short, they think he used steroids intentionally and often, contrary to his testimony.
The Mitchell Report is an investigation commissioned by Bud Selig and MLB. It is not the be all and end all investigation of every Major League ballplayer who has used. And it is not the sum of the entire evidence against Bonds. It is the sum of the evidence gathered by Mitchell, who was significantly handicapped in his ability to gather info. (He couldn't subpoena, for example, any MLB players to provide information. Those that did, did so by their own personal choice.. and against strong urging by the Player's Union). It wasn't a criminal investigation. Mitchell had no real authority.
In short, the Mitchell Report does not prove anyone innocent. It doesn't lift the suspicion off of anyone. It doesn't clear anyone's name. It only provides a tiny glimpse into a much bigger problem.