I've been looking for stuff like that aswell. Fb and documenting :/
As for the primary purpose of your application will not be to link to a third party application: I presume they mean, not just a canvas app with a redirect/framebreaker to the third party app/site. But something you actually use inside facebook.
Fb wants you to use its own advertisements, this used to be more of a privacy thing, because a lot of advertising networks use tracking cookies etc and this conflicts with the FB Privacy Policy. But since they went public, i'm guessing they need to show some ad income.
If for example, you have an app and as a bonus they get a point for every time they buy something, they get a discount or every time they unlock an achievement or w/e. it should not be a problem.
I do advise you to contact FB directly tho, just to be sure... response can be slow (weeks).