The Alliance won the war for Ala Mhigo because the Empire seems limited to one capital ship (Agrius and Gration), and because Zenos was more interested in getting an enjoyable fight out of it than actually winning. He had the Resistance cornered in Rhalgr's Reach, but let us walk because he was intrigued by our potential (or was simply too bored to care).

Midgardsormr's reason for stopping the Agrius remains unknown. Hraesvelgr only ferried Ysayle to Azys Lla because he acknowledged her desire to atone for her sins; Ysayle (as Shiva) disabled the Gration's engines (and the engines alone), seemingly indefinitely. (And also got herself killed, which to me is not atonement... but I digress.)