I still think the Feds knew about section 31 being behind this (simply because Bahir told them). But if the parliament debates over this, wouldn't the world know about this whole affair afterwards? Or are those secret deliberations only high ranking military people like Sisko know about?
The thing about bacteria is that they don't enjoy human rights, but STVI for example leads us to believe that (most?) sentient aliens enjoy those rights in the Trek future as well (and I can see how the Borg could be counted as an exception).