Okay, so, I watched Year of Hell, and then skipped forward to episode 6.18, the Lindsay Ballard episode, so, I could see what everyone is talking about. I don't see the problem, or Janeway's inconsistency.
Capt Picard and Annika were assimilated
Neelix and Tuvok were merged
None of them actually died, they were still retrievable
Crusher tried and succeeded in De-assimilating Capt. Picard, and the EMH did likewise with Annika
The EMH was able to de-merge Neelix and Tuvok
In Lindsay Ballard's case, she died on an Away Mission, the EMH was unable to bring her back to life. Voyager had a Funeral Service for her, and buried her in space.
Another species found her corpse, reanimated it, changed it's genetics and placed another personality into it. This should have resulted in Lindsay Ballard personality being lost, but, her memory still partially survived and she returned to Voyager for Sanctuary, and was granted it
The EMH tried to restore Lindsay completely, but, was unsuccessful in removing the Kobari Genetic changes. His partial efforts were less successful than he realized, and the Kobari personality started reasserting itself, and he would have to treat her several times a day, for the rest of her life. Lindsay couldn't handle that, and realized she didn't belong on Voyager, and there was no cure. Lindsay (not the Kobari personality) decided she couldn't live like this, she couldn't even do her job with the EMH providing her treatment several times a day. Lindsay decided to leave Voyager and allow the Kobari personality to take over.
So, Janeway made the same decision for Lindsay, that she did for Neelix, Tuvok and Annika, she gave precedence to the claim on the body to the original personality. Tuvok, Neelix and Annika were all successfully cured (and never died). The attempt to cure Lindsay failed, she was dead, unable to be restored, and the Lindsay personality was fading away, despite the attempts to cure her. Nothing more could be done, she honored Lindsay's request to be allowed to die again and let the Kobari personality take over. if Lindsay hadn't made that decision, the Kobari personality would still have taken over, but, Lindsay wouldn't have a chance to say goodbye to everyone and her Kobari personality would've been stuck on Voyager and felt out of place.