How so? Chekov is contextually specifying a difference in the treatments of himself and Valeris: "they might have" but in this case didn't, despite the shared feelings. Grammar doesn't touch on that at all.
In any case, all this talk about prosecution is beside the point, as the heroes have no plot reason to discuss Valeris or the conspiracy. They are worried about their own fates here, and rightly so. The conspiracy probably won't be wrapped up within the confines of the movie, or even within the lifetimes of most of the characters. The antagonism with Klingons has no end in sight, either. But prosecution of our heroes, on whatever charges (Uhura's are imaginary, a mere sigh of relief rather than a tackling of the actual issues the heroes might have faced for their mutiny, sabotage and whatnot) is the currently relevant issue.
Timo Saloniemi