I always got the impression that the Kirks were both destined to wither away and die if kept separate, but it's been a while so I might be wrong there.
There's also the issue that EvilKirk was a danger to everyone else on the ship. You could make the argument that if he survived, he could have learned to control his behaviour, but I'm not sure that's the case for a personality entirely made up of those negative traits.
It's definitely a moral grey area, whereas with the Tuvix situation it's more black and white. There was no danger to anyone else, he was well-liked and a credit to the ship, there was basically no reason for Janeway to split him back apart other than "I want to".