Marketplace on top of an iOS app? Is it possible to write an app for the iOS App Store, where developers can write Web apps to run on the top of your app. The developer's app will run in a Web View that has been injected with a cookie with session information about the user logged into your app.

At the end of the day, this is just a Web browser with no native capabilities. So, I was wondering if Apple could deny the app, because it is messing with their profits? If so, what if you did some sort of token system where a user could buy token's through an In-App Purchase that they can then use to purchase apps on your market place?
Yes, it is possible to write such an app. It is actually very simple as what you're describing is really just a specialised form of an ordinary web browser. You'll find multiple browser apps on the App Store, so these apps are well established.

Yes, Apple could possibly deny such an app from being listed on the App Store. It is their store after all, so in theory they have the possibility of denying any app. This is not the same as saying that this app will be denied - not at all.

Yes, it is possible to create such a "token system". Apple explicitly details that in-app purchases can be used for in app currencies or "credits", and that these can be used to "tip" digital content providers.

All in all, from your description it seems unlikely that your app idea will be approved on the App Store. Apple explicitly forbids creating an app that is really just an interface for displaying third party apps similar to the App Store. Apple also explicitly forbids creating apps that download and run code for running other apps inside an app. 

Whether or not your idea is a forbidden App Store competitor, or it is an allowed "curated web browser" really depends on the execution of your idea.