Re: most "wrong" episode...
The Federation preaches non interference when it involves other culture's problems, but when its freedom is threatened they sometimes throw the rule book out the window.
The Fed got frustrated when the Romulans didn't want to get involved in the Dominion war, so they tricked them into it on their side.
If they were winning it probably wouldn't have bothered them as much, but since they were losing, they didn't care about non interference.
Your ethics don't do you much good if you cease to exist as a society. Federation historians and philosophers may look unfavorably on Sisko's actions, but they'll be able to pass those judgements in a free society because of those same actions.
"...the most elementary and valuable statement in science, the beginning of wisdom, is I do not know." - Lt. Commander Data, "Where Silence Has Lease"