I would break the rule of this thread and recast him.
If however, I was forced to keep Beltran, I would have Chakotay lead an away team on an 'routine' exploration and gathering mission. The planet would have a relatively safe flatland section, and a valley area that the sensors showed was populated with dangerous predatorial animals. Janeway would order Chakotay to keep the away team in the safe area. Communications would be lost for some reason that is convenient for advancing the plot.
Neelix would report that the plains section was great for harvesting roots and vegetables, but that scans of the valley showed that it contained fruit trees and promised he could make delicious juices and pies if he was allowed to harvest there. Chakotay would say "I'm in command. This is my mission. We enter the valley, secure the fruit, return here, and then beam up". After a brief objection by some random members of the away team, Chakotay would assert: "This is my mission. Either you do what I say or we settle this the old-fashioned way". Thus inspired by Chakotay's firm and inspirational leadership, the away team heads into the valley.
All goes well until Neelix is killed and eaten by one of the predatorial animals. Chakotay orders a retreat, but Vorrik (Vorik? Voric?), the crewman who used to be an engineer on the Equinox, and a well-liked former Maquis security officer are killed while fleeing. By the time the away team gets to safety (the animals for some reason don't want to leave the valley), only four people are left: Chakotay, Ensign Samantha Wildman (can't kill her off because the episode would then be dominated by Naomi Wildman's grief), Ensign Harry Kim, and another random security officer). Once safely back in the plains area, Ensign Wildman somehow re-establishes contact and the four of them are beamed back to the ship.
This time, there can be no simple reaction like absolute ignorance, putting Chakotay 'on report', or confining him to quarters for a few days. No, this time, Janeway reacts with justified anger. She relieves Chakotay of all rank and position and then throws him into the brig. She also blames herself for not having reacted more strongly to his previous rule-breaking.
This time, there is no reconciliation. She keeps Chakotay in the brig until she finds a populated planet. She dumps him there. The former Maquis do not revolt, in part because they are angered at the death of the security officer. Voyager leaves.
The next episode deals with anger, grief, and the needed recruitment of new crew members.
Chakotay is never again seen nor heard in the entire series, nor in any other star trek series.