It's a ***** of a mission, ain't it? I'm currently replaying the whole game again, and dreaded this mission, which I am now stuck in.
Sadly, this mission is a matter of luck and speed. About the only way to defeat this mission is to blow away the Hurrim as quickly as possible as soon as they change sides. (Press the 'r' key repeatedly right around that point so you can safely fire on the Hurrim without disqualifying yourself). Doesn't end there, though, then you gotta race ahead to the Alliance ships who are slow to hyper out being attacked by ties. You have to take care of those pests too.
A quick way to beat this mission is to fire-link your ion cannons and lasers, this makes short work of the enemies. To make things a bit easier, go invulnerable and unlimited weapons (you wouldn't have to worry about recharging lasers unless you reconfigure it) and bump all the shield energy into the engines to make the pathetically slow Y-wings pick up more speed. Don't forget the "[" key which reduces power to 1/3, but enables you to turn quickly. Use this briefly to get your enemy in the visual field of fire, then go back up to full throttle to shake off additional enemies on your tail.
Much luck, I'm still struggling with it, so don't feel bad.