My very first post at the TrekBBS was an alternate version of the series finale back in 1999... I don't even remember what it was anymore though 
Anyway I'm in the middle of my first rewatch of the series since it went off the air and I just finished "Sacrifice of Angels", my all time favorite episode.
To me it's the high point of the series, and everything is a little downhill afterwards. Not that I didn't enjoy S6-7, but it just lacked a certain something that S4-5 had.
The biggest problem with the last two years, of course, is Psycho Dukat and the Pagh Wraiths. So here's my take:
At the end of "Angels", Sisko gets the Prophets to close the wormhole, Damar kills Ziyal, and Dukat snaps.
BUT: here Dukat snaps by killing Damar and goes back with Weyoun to Cardassia to remain the leader. However now he's just completely unhinged and willing to wipe out Bajor and the Federation. So he's a darker more violent version of the character willing to follow the Dominion.
And Sisko's penance for the Prophets' aid? It's not something they intentionally do to him. The consequence of the Prophets intervening in mortal affairs unleashes the Pagh Wraiths to action.
They form some kind of alliance with the Dominion. They get to kill the Prophets, and the Dominion gets their wormhole back home for reinforcements.
The series finale would be a massive battle at DS9 as the Dominion and the Wraiths go for the wormhole to kill the Prophets.

Anyway I'm in the middle of my first rewatch of the series since it went off the air and I just finished "Sacrifice of Angels", my all time favorite episode.
To me it's the high point of the series, and everything is a little downhill afterwards. Not that I didn't enjoy S6-7, but it just lacked a certain something that S4-5 had.
The biggest problem with the last two years, of course, is Psycho Dukat and the Pagh Wraiths. So here's my take:
At the end of "Angels", Sisko gets the Prophets to close the wormhole, Damar kills Ziyal, and Dukat snaps.
BUT: here Dukat snaps by killing Damar and goes back with Weyoun to Cardassia to remain the leader. However now he's just completely unhinged and willing to wipe out Bajor and the Federation. So he's a darker more violent version of the character willing to follow the Dominion.
And Sisko's penance for the Prophets' aid? It's not something they intentionally do to him. The consequence of the Prophets intervening in mortal affairs unleashes the Pagh Wraiths to action.
They form some kind of alliance with the Dominion. They get to kill the Prophets, and the Dominion gets their wormhole back home for reinforcements.
The series finale would be a massive battle at DS9 as the Dominion and the Wraiths go for the wormhole to kill the Prophets.