Again, you have very valid points, what we did in a lot of our Apocalypse games was = if a super heavy moved over a piece of terrain, like a building, it was destroyed and removed from the table. if we had sufficient rubble area terrain laying around we would put that in its place and now it was difficult and dangerous terrain for all other units. but different game mechanics and all, I get that.
Now, as to the rebels not getting a huge hulk of a tank or something else equivalent to the AT-AT, the rebels do not have access to the same level of equipment the empire does. that's why there is this feeling that the empire is unstoppable and such a daunting war machine.
as slow as the AT-AT would be in this game, lumber some at best. I would see its top speed moving it 1 at the most a turn, with a special pivot tool. this would essential make it a walking bunker that might move 12 inches the entire game.
now the point that I keep forgetting to make, the rebels "super unit" IMO would be something more like clone wars era vehicles, or heavy repulsor vehicles that are quick but lightly armored. lower points cost but would perform a whole lot different.
also, side note, I feel that because of the nature of the rebels, they should be allowed to take AT-ST's and other imperial vehicles, because, well, they are rebel scum of course.