Mr. Rate: Would've been a bad job to take, though.
Nick Memphis: How come?
Mr. Rate: Whoever took that shot's probably dead now. That's how conspiracy works. Them boys on the grassy knoll, they were dead within three hours. Buried in the damn desert. Unmarked graves out past Terlingua.
Nick Memphis: And you know this for a fact?
Mr. Rate: Still got the shovel.
Bob Lee Swagger: I was kinda hopin' to keep one of 'em alive, but they were determined to kill you.
Bob Lee Swagger: Not bad for a poodle shooter with a makeshift silencer, huh?
Answer: You are completely correct. This is a clear mistake, the colonel could (and would) most certainly be charged for his crimes.
BaconIsMyBFF
Though unlike the movie, it's not up the attorney to decide if a military member gets charged, it's up to the judge advocate general.
Actually it's not a mistake. The colonel is not a member on active duty in the service. He's ex military. He's the one running the contractor group that carries out the senator's dirty deeds.