Yes but Tom broke HER rules. Janeway just breaks far away starfleet rules (and gives her crew opportunities to object and have it noted). You can't have complete insubordination. I suspect he would have been more harshly treated back in the Alpha quadrant but it would be bad for crew morale to do so.
I say screw Janeway and her ridiculous rules. I applaud Tom for showing courage and trying to do what he believed was right. He handled the situation extremely well. I would have acted no differently.
I supposed the Caretaker felt that way before his tampering with a biosphere destroyed an enter ecosystem.
The person that represented the entire body of that civilization told Janeway and Tom "No". Tom listens to the guy that had the representation of nobody.
That government could see such a thing as an act of terrorism. Tom would have gotten everyone on Voyager executed.
If Janeway breaks a rule of government, sh would ask that only she be blamed and negotiate her crew be released. Tom as a crewman has no such barginning chip. His actions doom everyone.