I hate Janeway as much as the next guy, but every Star Trek captain has contradicted himself at some point. Every series has at least one episode where you go: wait a minute, wasn't he on the exact opposite side of this issue a few seasons ago.
An example that comes easily to mind because I was recently reminded of it: in the movie Insurrection, Picard (and his crew) defy a Starfleet Admiral to save people who Starfleet is planning to relocate against their will in order to give their planet to another power. There is an episode in the seventh season of TNG (Journey's End) where Picard is cast in the role of that Admiral, enforcing the order of Starfleet Command to relocate those people, and Wesley Crusher is in the role of Picard, disobeying that order and trying to save the people's right to their homes. And Picard dresses Wesley down for his actions, saying that "You defied the orders of the ranking officer on the scene", and describing that as "unacceptable". When Wesley offered in his defense that the orders were "wrong", that even though they came to Worf from Picard, to Picard from Admiral Necheyev, and to the Admiral from Starfleet Command, they were still wrong, Picard's response is "That decision is not yours to make".
Now, the two situations are not directly parallel: the Baku were not being removed against their will, they were in fact being removed without their knowledge. And they weren't Federation citizens to begin with. And Picard made a point of removing his uniform before beginning his rebellion, which matches his comment in that episode "While you wear that uniform, you will obey every order you're given and you will conform to Starfleet regulations and rules of conduct".
Similarly, the situations Janeway faced were not directly parallel. Quinn managed to convince her that he was indeed rational: that his desire for suicide was not a symptom of mental instability. He convinced her that he was in his right mind, or as much so as his circumstance would permit, and that his desire to end his existence was born of a desire to use that as an instrument of change, as a political statement in essence.
Seven, however, was clearly under the influence of aliens known to use mind control. Perhaps Janeway should not have been so dismissive of her expressed wishes, but her reaction should have basically been "Once I am convinced you are not under the influence of any kind of mind control or insanity, if that is still your desire I will see to it that it is arranged." And there should have been a follow-up (perhaps in a later episode) where Seven says that she no longer would prefer destruction or re-assimilation to remaining on Voyager.
