the main reason is probably that the chip is already outputting the image in a lossy format, and if you reorder the pixels you must reencode the image which means degrading the image, so it's much better to just change the exif orientation.
JPEG can be rotated losslessly. `jpegtran` can do it, for example (and comes with a script called `exifautotran` to automatically normalise the orientation of a bunch of JPEG files at once).
