Yes. Prior to any control point optimization, enter an Image
Orientation 90 degree roll value at the Camera and Lens pane for the
images you want to see as rotated in the Control Points pane.
Remember to zero these values out prior to performing control point
optimization. If you run into trouble, for example if the stitch runs
way out of control, then zero out all the Image Orientation values
for all the images and then re-optimize.