Guys, Bones was making a funny. It's supposed to be a wiseass sarcastic answer, not a serious comment about being let off the hook for anything. It's pretty much understood they saved the galaxy and nobody's gonna punish them for anything they did on the way to winning.
De Kelley delivered it as he would a punchline. "We saved civilization (again) and we got away with it." Sarcasm. His follow up line was also said by Kelley as a joke:
McCOY (looking at Spock)
Well, they don't arrest people for having feelings.
When he said the "prosecute" line, people in the audience laughed. Not much, it ain't that funny, but it's in keeping with Star Trek 6's "give Bones a wisecrack every 5 minutes" scripting. Honestly, I think you guys are looking too deeply into it.