Except the episode shows that Sisko challenged himself doing which showed why he felt it was so bad and why he also justfied it.
Tuvix does no such thing.
It goes from the crew liking Tuvix, Tuvix preferring their existence, to Janeway suddenly forcing a precedure. It doesn't show Janeway wracked with dealing with the ethical dilemmas nor show any hint of introspection. Tuvix says they have a right to live and then Janeway is just like,"NO YOU DONT".
Then, at the climax, Janeway applied the precedure on Tuvix under armed guard against their own will which the doctor himself refused to do for ethical reasons all while looking like a emotionless robot while doing so.
This is compounded with the fact that much of S2 has Janeway regularly saying that they won't sacrifice Federation ideals. Then the episode hits a nice, big reset button.
Comparing this
With Tuvix is illogical.
One has self awareness and acknowledges going against ones values. The other the captain just does whatever because she wants her friend back.