you don't need to batch rotate - in order to stack you have to register. as long as your registration reference has the orientation that you want, the registered frames will be rotated to match. so if you rotated just the reference frame and wrote it to disk, all the other frames would end up with the same orientation.
but it kind of doesn't matter since no matter what orientation the images are during stacking, you can always rotate the stacked result to the angle you want.
but if you still want to rotate a batch of images, you can use ImageContainer to automate the rotation.