I think that patching on a turn roll is a good idea. Changing in the middle of a turn is unlikely to result in an advantage or disadvantage, but the fewer things there are to make claims about the better.
I suggest that MS (most likely HUSch) should stay online after hitting enter, and pause when it starts taking inputs again. Then PM me to say it's ready (I'll get a notification on my Blackberry) and I'll start it back up on the new patch level, unpause, and post in the tracker thread.