Exactly. It's really not that complicated and is laid out pretty simply for the audience, if you think about it.
McCoy says "And the good news is they're not going to prosecute!"
Audience says "Huh? Not prosecute who?"
Immediately afterward, Uhura says " They might as well have prosecuted me. I felt like Lieutenant Valeris."
Audience says "OH! Valeris was let off the hook. Good. We liked her and were upset that she became a bad guy, but feel better now that all is forgiven. It's a happy ending after all."
It's more like:
McCoy says "And the good news is they're not going to prosecute!"
Audience says "Why would they prosecute the heroes? What did they do?"
Immediately afterward, Uhura says " They might as well have prosecuted me. I felt like Lieutenant Valeris."
Audience says "OH! Valeris is getting prosecuted. Good. She betrayed her oath and everything Starfleet stands for to get revenge on Klingons who never did anything to her. Good riddance."
It astounds me how many FANS complain about how obvious Valeris was as the mole/traitor in the crew, yet non-fans have no problem with it, because they just don't make the connection with Saavik, and don't need it. The story is entertaining for them as it is.