It is safe to isolate a DC like that but really not needed and in fact not even recommended anymore. Take a look at the DS team mail sack from last month
http://blogs.technet.com/b/askds/archive/2010/04/16/friday-mail-sack-i-live-again-edition.aspx
See tje question is there anyway to isolate a DC...
You can also run into USN rollback issues with snapshots.
I've yet to hear of an adprep for 2008 doing damage to an AD...at this point it has been done thousands of times on various networks. If there was a major issue it would have surfaced by now.
Thanks
Mike