I just test this out in skimish, and your correct. Though you can counter the slow moving AT-ATs with either IG-227 Hailfire-class Droid Tank from range or Low Altitude Assault Transport/infantry (so long as you stay behind it). Or in a pitch by microing your infantry, as the AT-ATs can't turn around fast enough to target them. The AI rarely escorts these mammoths, so just stay aware and try and see if any AT-ATs are in the unit stack before entering land combat. Do try to have a good and reflexable range of garrison of units.
I do understand it can be very frustating at times dealing with large bunch of these buggers. But, the best way of dealing with them is taking the fight to them, inflict alot of damage on them before they reach your defenses and your turos should give a good fight before going down.
I hope this helps some.
Corey, I found I couldn't build AT-TEs in skirmish as the PA. But I could build other units of the same 'tier' as the AT-TE, is this some kind of bug?