Arathi Basin currently takes 5 minutes to close if there aren't enough players, but it only takes 3 minutes to win if you 5-cap. I've been in multiple matches today of 15 horde vs 2 alliance, and it always ends the same way. Easy marks for the already dominant faction.
(Not complaining about faction balance, the auto-end timer is the issue.)
Sounds like you got unlucky. I've not run into this issue myself. However, this is the way it has always been with those timers even in retail tbc. So it is working as intended I believe.