As long as you're an Imperial Pilot (who can fix any damage from in the cockpit), Vanguard's missiles really shouldn't be a bother. They'll sooner run out of missiles or be sniped before they can do any real damage. Usually if a Vanguard launches a missile at you, they're giving away their position, and are setting themselves up to be blown away by incoming cannon fire. The anti-vehicle cannons (dishes that fire yellow-orange blasts) can be a threat when all the cannons are concentrated on you, but one well-placed blast from the AT-AT main cannons will blow it to bits.
Other Rebel methods I've found sufficive are the Orbital Strikes called via Marksman's Recon Droids, and Vanguard's Mines (you can't avoid them if they've been placed underneath you). Although usually the Vanguard blows himself up when placing the mine (it blows up instantly, seeing the AT-AT
), they take out a good amount of the AT-AT's armor. I haven't tried using the Wookiee's Time Bombs, but I'm sure they're about as effective as Mines (and they don't blow up instantly, so the Wookiee has a chance to escape).
The main threat to AT-AT's is the Snowspeeder (only if there's a gunner to fire the tow cable of course). I've found it easy to shoot down the Snowspeeders as they're making their rounds. One direct hit from the main cannons will take down the Snowspeeder. So man the guns, pilots!