Similarly, I don't think in Janeway's case it needed to have been a full blown mutiny. Simply an outside alien who criticized something Janeway did or was about to do ('you'd better not meddle with <X>!')and was shown to be right in the end.
Arturis in "HOPE AND FEAR" gave us that alien critique.
He was right in that allying with the Borg essentially stopped them from getting eliminated by Species 8472. By doing that, all the races that were targeted by the Borg were going to get assimilated, which is exactly what happened to Arturis' people. And who knows how many others. (We know of at least one race being fully assimilated, in "DARK FRONTIER".)
He was proven to be right as far back as "SCORPION, PART II" because the Borg invaded
their space, thinking they could get a new species assimilated. That backfired, and 8472 invaded us.
Despite this action giving us Seven of Nine, which is one of the best characters in the franchise, it was the wrong thing to do. Chakotay was right... an alliance with a group guilty of killing and assimilating
billions of people, possible a trillion or more, is wrong.
I definitely call her allying with the Borg one of THE worst things any of our captains have done.
Regarding the comparison with Picard and Sisko, I don't think they can be compared on the same level.
When Q flung the
Enterprise to the Borg, he did it to teach a lesson two levels. First, to show Picard he was not ready. Second, to basically do them the favor of
getting ready. One of the reasons why Picard was never seen negatively here is because of what Q said... it's difficult to admit you need help. He got past his arrogance and did the one thing an arrogant person does not do... ask for help. That is seen not only as a positive, but as growth. Plus, Q started the whole incident, and Picard knew he would be the only one to end it.
The Sisko comparison with the Maquis planet... he took an action to stop a terrorist group from killing millions along the DMZ. While the ethics of it can be debated (I firmly believe he made the right call), he did it to
stop a group from murdering more. Despite the method, it served a greater good. That can be seen as a positive.
What Janeway did... she
helped a group to survive so they can keep on murdering AND assimilating more. And on a
MUCH larger scale than the Maquis could ever hope to be capable of doing. THAT is a negative.
If you want a comparison of Janeway there with another captain that might work on a similar level, I'll give you one.
Kirk's decision at the end of "A PRIVATE LITTLE WAR". By providing weapons to the Hill People, he basically helped to guarantee fighting between them and the Villagers for who knows how long. Perhaps decades. There was enough evidence to prove the Klingons' involvement, but that wasn't enough for Kirk. I understand he was trying to stop the Hill People from getting killed by teaching them about the flintlocks, but all that did was condemn both sides to bitter wars.