The walls are only a hologram...so they can be passed through with the Ragnarok. The Garden can't pass through it because the pilot sees the wall and assumes that it would be impossible to pass through it (as you would, I mean it looks pretty solid…). Obviously, no one is going to fly the Garden into a wall and destroy it on the off chance that it WAS a hologram (an occurrence that no one knows about at first…) so the Garden stops before it breaches the walls.

Can’t remember if you can get the Garden back after you have been to Estar, but if you can, the same sort of thing would apply. Even if Squall DID tell the pilot that the walls were a hologram, I doubt that it would entice them into doing something as ludicrous as flying the Garden into it. I mean, just the sight of the Garden moving towards the wall would be enough to give half the students heart failure. Of course, the Ragnarok is piloted by Selphie and since:

1. She’s seen first hand that the walls are holographic, and
2. She’s an insane, war mongering bitch,
She might be more incline to fly straight through it….

Think that covers everything.