'Voyager' actors Ethan Phillips, Tim Russ, Garrett Wang, Robert Duncan McNeill, guest star Tom Wright, and writer Lisa Klink talked "Tuvix" at Trek Talks 3.
Yeah, he was largely operating in safe space and still made some unethical decisions.
Janeway was willing to make the hard calls that would best serve her ship and it's future, having your cook and your third in command get fused isn't exactly going to result in a functioning chain of command.
Plus since the operation could be reversed, you could argue that Tuvok and Neelix aren't actually dead, merely suspended animation like storing people in a transporter buffer. You're still killing Tuvix, but sacrificing one to save two is "the needs of the many" in it's most simplistic form even without the added weight of hundreds of lives depending on Tuvok's leadership and tactical skills.
I never once considered Janeway to be out of line given her circumstances. The crew always comes first even at the cost of her own humanity and ethics. She's a good captain, willing to make the call that ends lives and live with it so that others may not have to endure those decisions and consequences. She didn't ask anyone else to do that for her.
I mean, DS9 was almost as much in the boonies as Voyager. Assistance was limited, and there were limitations on what he could do, as he was only running the station at the behest of the Bajoran government, not as a true representative of the Federation.
It also introduced facets of war, even before it became a full blown thing in the later seasons. He wasn't always on the side of the angels... because there are no angels in war. War only ever makes demons.
It doesn't excuse his actions, but it doesn't make them truly inexcusable either. They both operated in much more of a grey area than either of the two previous series.
Bajoran space was far away but not impossibly so from Federation resources, I'm not trying to say he's a bad Captain, merely that the comparison to Janeway is a complete farce. If we are being fair they both fail to uphold the federation's ideals.
If we are being reasonable, they both did what they had to do in order to save lives and get the job done.
My issue is the constant Trekky tendency to pretend Janeway is a shit bag and Sisko is somehow better, it's just bias.
There are a lot of instances where the Enterprise crew wanted to do the ethical thing, and Picard stops it or tries to. For example, when Dr. Crusher wanted to help when that planet population was addicted to drugs, and Picard wouldn't let her do that or communicate anything to them.
Also, Data once found humans frozen in space, and when he helped them, Picard was annoyed; it wasn't even a Prime Directive issue!
I believe the only reason nothing happened to him was because of Bajor, with him being seen as an Emissary to the Bajoran people, punishing Sisko would Punishing the Prophets chosen one, they wanted Bajor in the federation no matter what, that was the end goal, so leaving Sisko essentially unpunished was right for the greater goal of bringing in Bajor.