Considering how many really bad men have been taken off the files by Tony, it is very possible that Agent Harris considers him to be an asset. Ralphie, Chrissy, Pussy, Jackie Jr., Jason, Patsie's brother, Junior, Vito, Richie, Big Dom...etc.
Tony seems to be doing his job for him, without using up too much of the taxpayers money on trials, other than what has been spent on Uncle Junior's trial.
Harris made it very apparent that he didn't like Phil at all. Open door to kill him off also. Johnny Sak, is gone. These other guys are so old that they will eventually blow away if they are not given an opportunity to pass their ways down to the next generation.
Junior mafia, Parisi and Carlos' kid may be a problem. AJ is out of circulation and the older generation is taking itself out.
Maybe Harris is using Tony like a weapon, aiming him at anyone who the feds would like to see gone.