If he wanted to leave Ethiopia and seek asylum in Switzerland, it's unlikely he could do it coming over the border on a train. He'd need to land in Switzerland direct. Would Italy have been an asylum option for him? If so, then all he had to do was chat to the nice immigration police after his regular arrival, and could ask to talk to them privately away from the rest of the crew. They could feign his detention if necessary.
Flying solo, when other crew resources were available, all the way from Sudan to Geneva, going several hundred nm beyond his intended destination into mountains in winter? I would think that the Swiss prosecutor could find something in the recklessness book to cover that. The first officer's insanity defense would look promising though.
It's not as clear cut for hijacking as some non-crew person threatening the crew or occupying the flight deck, but without a good excuse - he thought that the captain went gaga, he thought someone was trying to bring the captain into the flight deck from the bathroom as a hostage - I don't see a non-mental excuse for locking the door being valid. If the first officer thought that the aircraft was at risk from the captain or others on board, then surely his natural role would be to land as soon as possible to prevent that - in Sudan not Switzerland.
If an armed person on board had shot the only trained crew member at the controls, while nothing untoward was happening? I think the Swiss prosecutor would also have something in the recklessness book for him too.
Whatever weirdness was going on on board (and it would not be clear what it was, given they could only talk with the first officer), I'd expect the Italian and Swiss air forces to take an interest in the aircraft.