If you commandeer an AT-ST you can damage the walker, and missiles will also damage the AT-AT, but it takes a LOOONG LOOONG time, (just like in SOTE game) compared to the tow cables.
Let me tell ya, having an AI pilot makes tripping up an AT-AT hard.
So save yourself the trouble and capture their AT-AT spawn point as soon as you can, though it is satisfying to trip up at least one for the "movie effect." ; )
Sadly, the Rebels can't commandeer the Empire's AT-AT's (just like the Droids can't take over the Republic AT-TE's), only the smaller walkers.
It's also too bad that you can't fire your blaster while riding a Taun Taun. In every other Star Wars game you can do that, but not in SWBF for some reason. I don't think there's any way to heal a Taun Taun is there?