something is wrong here - CR2 files are never stored by the camera in a rotated format. if you have the setting turned on in your camera and you are holding the camera rotated while taking a picture, a flag is written to the file's EXIF structure that indicates that the camera was rotated. display software is supposed to recognize this flag and display the image rotated. but the sensor data is always recorded with the long axis being the X axis.
the rotation flag has little use in astrophotography, and i'm pretty sure that PI ignores it. are you sure you aren't trying to combine CR2 and TIFF images? if you open a CR2 with a program that recognizes the flag and then save it out as TIFF or JPEG, it's possible that the rotation will be "baked in" to the TIFF/JPEG.
rob