I've no doubt that he would have been court martialed if there had been any deaths from his WMD. But the fact that there was none, coupled with the Federation's irrational hatred of the Maquis for daring to want to secede from the UFP, meant that nothing happened.
I think you've hit the nail on the head with the reason - there weren't any casualties to splay their faces all over the 21:00 Hours News (Not quite the same ring to it in the 24th century
) so the public wouldn't get their moral outrage up and running, and the planet was a Maquis base, so the Federation don't shed any tears over its loss. Which is hard to fathom, really - I realise Class M planets are rather stupidly easy to come by on Star Trek
but it seems a bit much to just overlook unleashing a wmd on one out of, essentially, angry revenge.
You also get the positive spin that can be placed on the fact that the displaced Cardassian colonists from the Maquis' initial surprise attack can apparently just swap planets with the Maquis colonists. That would have got the Feds some points from the Cardassian government, making Starfleet hesitate from taking action against Sisko lest it send the Cardassians the wrong message. Then you have Sisko's role as the Emissary to the Bajoran Prophets and if you imprision him or boot him out of service relations with the Bajorans could be damaged. Bajoran could just recruit him into their Militia order Starfleet out of Deep Space 9, or say that they want a Bajoran militia officer in command and Sisko could be back in command of the station and if Starfleet still has a presence, they would be then at his whim and no longer have any control over him or his actions.
Even though there were no deaths, the potential for them was definitely there if ANYTHING had gone wrong. Those Cardassians on the evacuating ship almost died. While that wasn't Sisko's doing, who knows what could've gone wrong with the Maquis evacuation--and don't forget, we can't prove everyone on that planet was a Maquis sympathizer. Some people may have just been there with family. So innocent people, and children get run out of their homes because a nutter decides to launch a WMD? I don't think so.
And switch planets? So? Both people got run out of the place they were calling home
. And who knows what was done to the ecosystems of those planets? Are they even getting planets that are going to be any use to them?