Yeah, a weirdstone, and shaped antimagic fields, with magical locks inside holes in the field (or cast by a sufficiently awesome/red wizard boosted Cleric of Mystra) is a pretty foolproof way to make something not easily accessible. Riverine or Obdurium doors helps in that, too, especially with magic traps of Repair Object firing every turn to mean you have to shatter them all at once. Putting an antimagic field over the door so you have to shatter it without buffs makes it even harder. The walls of the place should all be like this, so you can't just dig your way in either.
They should also ideally be backed by permanent walls of force/cased in permanent walls of force, so people have to try to dispel a wall of force inside an antimagic field in order to get in.
Disintegrate will do it, though.
If you want to make disintegrate hard to do, have magic traps that every turn fire up dozens of 'wall of ice' or whatever in front of the real wall, so you can't easily disintegrate it from range, you have to enter the AMF to even be able to LoS the door.