For me it was always obvious.

I mean, Janeway was thrown into a hostile environment with basically nothing, and sometimes picked the less moral choices, to make her crew survive.

Sisko decided to ruin the lives of basically a whole planet, just because he was to arrogant to admit that he got defeated.

I think there’s a matter of context, and Sisko has no way to justify his behaviour other than “I see myself as god so I can do whatever I want”