The opening battle was a good hook for new viewers and forgivable because the show never had the Borg appear in a stunt like that again. Also, by having the Borg kill Sisko's wife it meant they had more impact in their DS9 cameo than in the entirety of their run on Voyager.
My favourite parts in Emissary are Sisko's meeting with the Prophets. It's a plotline I dislike in the final season but it's perfectly handled at the beginning. Very smart science-fiction.