Have the tornado carry a couple of trees or noticeable objects from the surrounding area, only to throw them at the fortress, maybe smashing a wall or large window. Don't have the damage just be "it hurts you." make it so that the tree destroys a wall and then becomes part of the terrain and...
Pathfinder is facing the same problem that 3.5 did. As the game expands, the amount of errors in judgement expand too. It's not a problem if you are able to pick up the game from the beginning, and adjust or remove percieved errors for your group as the game goes on, but it can start to be...
One way to represent this in game might be to make it so that guns don't ignore the AC of Adamantine armor, or natural armor of creatures with DR/Adamantine.
It's a not a very good simulacrum, but I like anything that gives adamantine a use as something outside of being the material for high...