I think it's a good idea, but probably a little underpowered.
Consider the Dark Blue Rhomboid Ioun Stone (which provides Alertness), at a cost of 8000gp. Regardless of the relative worth of Alertness and Toughness, it's inconsistent for Ioun Stones with the same effect (grants a feat) to be different prices.
Then we've got the Pink Rhomboid, which provides a +2 Constitution bonus. Now, of course, this isn't the same thing as Toughness - you can be wearing a +Con item and have the Ioun Stone for more - but it's generally more useful.
I think your Ioun Stone should cost no more than 8000gp. For consistency, it should share the same prerequisites and statistics as other Ioun Stones (12th caster level, 12th level to create).
IMC, I'd ad hoc adjust the price down to 6000gp.
As an aside, Anubis's "proper" Toughness feats don't seem to be canon. They may be a good idea, but they're not official. Clearly, in Anubis's campaign, this Ioun Stone would provide +5HP when in use, though for ease of presentation, the item shouldn't propose a "fix" to other sections of the rules.