Facebook runs ads and tracking inside the Facebook app. Apple isn't stopping them from doing that, it's just making users aware of how that sausage is made. It's not like they are showing their own ads inside of the Facebook app.
The App Store today is barely any less skeevy that app stores of old, like GetJar.com or whatever I was downloading apps on for my Win Mobile 6.1 BlackJack phone in 2007. If they choose to weigh it down with even more ads, that's their prerogative.