It was a simple legal case.
One week earlier Janeway broke the Prime Directive in the Thaw.
The Natural development of the Khol was extinction.
They were morons who deserved what they got, and any attempt to save them, which is what Janeway did, would lead to these monkeys taking their AI technology to other planets, or taking apart the planets defences (the clown) could lead to other looters taking Khol AI technology to other planets.
The Clown, was every bit the threat the Borg was, if it was allowed free reign of the galaxy as it created it's own massive collective.
The Clown was the gestalt of a few peoples psyches, just like Tuvix. Murdering the clown and murdering Tuvix are identical crimes, a crime which no one thought to charge Janeway with, and therefore not a crime?
A week before that Tuvok should have been charged with grave robbing and kidnapping, and there fore lost his commission, and therefore reduced the power Janeway had over him. of course he could have insisted that he's extradited to face Drayan justice more properly than they had had administered ad hoc the first time around, which could have tripled his lifespan.
Actually, committing any crime, should have meant a trial, and delayed his execution.
You know, except that Janeway plays out trials on Voyager in her minds eye.
Tuvok was a Maquis (Sure immunity for his crimes was probably guaranteed, but it didn't seem like he'd been given his immunity, or any of the Maquis had been formerly charged or processed or put on a binding road to rehabilitation/reinstatement as free citizens.).
Therefore a convict.
Therefore protected.
Any attempt to kill him is as good as a jail break,and therefore Janeway needs to be charged as an accessory to illegal abscondment, and that goes double for Tuvix.
Chakotay is in Command for 2 seconds, and pardons the Maquis.
