Has anyone actually run into this problem? Is it a very unique environment that causes it?
In the early history of JkDefrag there have been a few people who have run into it, the postings must still be here on the forum. As far as I can remember nobody lost any serious data, only Windows data and no user data, and they all managed to repair their disk with checkdisk.
Are there any reasons MyDefrag should be considered potentially dangerous if used on a system with critical data?
In all the years that JkDefrag and MyDefrag have been in use there have been precious few reports about corrupted data. As far as I know these cases were all caused by other circumstances, usually a hardware problem. The Microsoft defragmentation API (and JkDefrag and MyDefrag) has proven to be extremely reliable. But just like Jonib says, it's always a good idea to backup, especially with critical data.