If you mean the rotation of the scale tool is not the same as the object then if you have frozen the transforms you can't line it back up, the only way would be to rotate your object back to verticle and the world then freeze the transformations again making the tool in line with the object.
If simply want to center the pivot on the object ,select the object and just go to Modify and then click on center pivot.
If you want to do something other than this then you need to explain more clearly what the problem is and what you want to do.