So in theory I could open the item in Nifscope, delete the mesh and save as a new object?
Yes, but not the mesh. You have to go up to Render -> Show Hidden to see the collision part of the mesh (it'll appear as non-textured simple version of the mesh). This is what you wanna delete. Just a warning though, if the wall piece is actually a side piece with a wall
and floor you'll need something more advanced than nifscope and delete just the wall part, otherwise you'll end up falling trough the floor before you get the chance to see the secret entrance (unless you want to make the entrance a secret trap for the player to fall in

).