Let's lay out the potential elements of a deal between Facebook and the publishers.
It might work like an app install. The first time you click on a link from a publisher that has opted in to its content being displayed on Facebook, you could be shown a big button to "Show content inside Facebook" and a checkbox to "Remember my choice".
Through the comprehensive Data Policy we all agree to by using Facebook it's very possible that not even that button is required for them to be able to share with publishers data in agregated form, equivalent to what you see on Google Analytics.
But, were it necessary, a list of the data you agree to be given to the publisher could be added below the button. Or alternately, permissions could be requested at the top of the article after it opens.
Afterwards, you should be able to access a list of your installed publishers to opt out if you want to.
In the interest of publishers keeping all their SEO juice, the API that Facebook provides publishers could allow for the implementation of the cross-domain rel="canonical" link element for handling legitimate cross-domain content duplication.
Disabling indexing wouldn't work; search engines have been incorporating links on social networks to their algorithms for a while. Publishers won't want to loose on that if what users link to is the article on Facebook and not the canonical version on their websites.
Another update: If later on, a publisher decides to stop hosting articles on Facebook, they should just redirect to the canonical article wiht the instruction that the content has moved permanently.
As Ben Thompson has already explained, Buzfeed-like publishers' strategy is perfectly aligned with the idea of showing content directly on Facebook.
And they wouldn't need to change their business model at all - as I've written before:
Buzzfeed and Buzzfeed-like publishers could keep charging for creating native-advertisements - now to be shown on Facebook; possibly without sharing revenue with Facebook.
Facebook could become a better Newstand for them. Selling subscriptions and keeping the 30% cut most app stores ask for. That would give Facebook the added benefit of accumulating customers' payment data. Which would in turn make them an even more atractive partner for this group of publishers and open a whole lot more revenue options for Mark Zuckerberg and company.
Additionaly, for those with porous paywalls, Facebook would become the ideal enforcer of the 10 article a month limit, given that it knows everyone's real identity.
This guys will get more and better targetted distribution for their articles as well as better targeted ads - though, with constraints.
As the Times article on the subject describes:
Although the revenue-sharing ideas are still in flux, one would allow publishers to show a single ad in a custom format within each Facebook article, according to one person with knowledge of the discussions.
This is Facebook teaching them how to do their business. By limiting inventory and better targetting, they are increasing the value of these ads.
While we don't know exactly what those ads will look like, unless they are an article within another article, they wouldn't qualify as native advertising. Just a better form of display ads.
As such, I don't expect them to be a game changer for this kind of publisher, but a life raft. They will be thankfull for it. And they will be glad to share money with Facebook. Whatever keeps them from drowning, on their way to the falls.
More on Why
On the reasoning why everyone should get on board with this, Dave Winer has been explaining it better than anyone for months already: