The left and right side of the last equation I gave represent the total pressure at two different points on the same stream line, and that is why you can equate them.
Strictly speaking we then assume that the streamline starts inside the store, gets accelerated by the tornado and then ends up passing outside the store window. If you are uncomfortable with that assumption, you may equally well assume that the stream line starts at a different place than inside the store, but with same static pressure (and height) and zero velocity.
And yes, once you have a pressure differential over the window and you know the area of the window you can calculate the net force of this pressure difference.