I think Tom Paris was perfect for Voyager!! I can't imagine having someone who has taken steps to hide the death of a fellow student and friend as well as convince his friends and fellow students to cover up the accident so that they wouldn't have to face any charges or explain themselves and the use of the banned maneuver. I don't believe he'd be trustworthy enough.

That's just my opinion.

I would imagine the doomsday machine just floated around in space dead, until it more than likely got pulled into a star by the star's gravity. Then it met its own doomsday. But that's just my thoughts.