Seriously. WHERE is the trial?! And you know if you are gonna take a while to get the trial together (since all the witnesses are dead) you put a man in prison while you wait. So he can confer with is lawyers.
What sort of horror filled Federation is this.. OH A BAD MAN, FREEZE HIM!!
The Federation wouldn't want a trial since Section 31 would have been exposed. They would want Khan killed, locked up forever, or put on ice. Maybe they gave him a choice?