I've got another spin on this.
In "The Visitor" Old Jake kills himself to bring his father back to life. I don't think anyone blames him for this decision, though depending on your view of quantum mechanics he just destroyed an entire timeline.
Now suppose someone decides that the timeline as shown isn't so hot and realizes that if Jake Sisko dies then Ben will be brought back to life and things might work out better for everyone. Are they justified in killing Jake to bring about this outcome? Heck, they're not even killing Jake per se; he'll be much happier with his dad around anyway, right? It's not Jake's fault that things have worked out the way they have either, he's just an unfortunate victim of circumstance.
You know, I think this is my root problem with Janeway's decision in the episode: I don't believe you should commit murder based on what you believe "the greatest good" is.