Surrounds are not as critical as your mains, but in theory, you should adjust the mic as you say when testing the surrounds. However, you have to move in and adjust the mic to the new alignment within the gaps between chirps. Audyssey is still recording during this period, and even the sound of you touching the mic might be enough to throw off the readings.
My surrounds are up high like yours. I used to try and re-align the mic between chirps, but now I just set it horizontal (pointing at the ceiling) for all speakers. I haven't really heard any noticeable difference - but then again, I don't have audiophile ears.