What the post doesn't seem to mention is that you can still read the data of your friends who also use the app if you store it yourself. So sites like JobFusion could continue to use the API, but won't be able to use the data of users who haven't opted into their service. Honestly, their shutdown post[1] is pretty laughable, given what they're complaining about.
It should also be noted that Facebook is going to app-specific IDs, which means that App A from company A can't share data with App B from company B, and the app-specific ID isn't your primary Facebook identifier.
There is a Business Mapping API that lets different Facebook apps from the same company share data, and theoretically Company A and Company B could collaborate on that.
[1] http://jobfusion.co/blog/no-more-referrals-fb-friends-api-sh...