I just checked Sony, Kobo, and Blio ebookstores, and The Sixth Discipline is still not free on any of them. I can find plenty of free Smashwords book in the Sony store, so I think they are just slow to make the change. The Kobo store doesn't seem to have any Smashwords books below 99¢, so I think they simply don't support price matching to $0.00. Blio doesn't have a good way to search or sort for free Smashwords books, and they are very new, so I have no clue what their policy is.
I guess time will tell.