Well, in WWII the pre-Vichy government had unconditionally surrendered in war to the German Army so either way the Germans were the legitimately recognized power there since they were adhering to the rules of war the world had established. France declared war, then lost, surrendered unconditionally. The Germans were within their rights as a sovereign nation to occupy France.
And we DO have to take into consideration the "Big Picture" here, it wasn't just about Bajor but about the Federation reaction to a world annexed by another power. Bajor was no different from any world conquered by the Klingons and Romulans, so whatever reaction the Feds have to them would also alert those others as to how the Feds deal with conquered worlds. If they do it for Bajor whose to say it won't happen to all other conquered worlds, the Klingons and Romulans would have new reason to distrust the Feds in that case.
And we DO have to take into consideration the "Big Picture" here, it wasn't just about Bajor but about the Federation reaction to a world annexed by another power. Bajor was no different from any world conquered by the Klingons and Romulans, so whatever reaction the Feds have to them would also alert those others as to how the Feds deal with conquered worlds. If they do it for Bajor whose to say it won't happen to all other conquered worlds, the Klingons and Romulans would have new reason to distrust the Feds in that case.