Part of the reason “Tuvix” is hard is because, at least superficially, Tuvix appears mentally competent, so it’s much harder to justify ignoring his wishes.
It also helps that both good and evil Kirk were slowly dying due to that traumatic separation, hence their need to be reintegrated before it was too late.
By comparison, Tuvix seemed stable, and there was no pressing need to have them be reintegrated before they both died. It seemed uncharacteristically spiteful to have him be forcefully dragged off to be separated with a risky procedure, whilst still begging for his life, with the only words Captain Janeway having about the situation being "sorry, I need my science officer back".