I'm not sure if this is a MP issue or a pro-sites issue.
We have a network set up with the front end site showing products from the whole network.
We also have Pro-Sites set up and run a monthly subscription to have a store.
If a store owner doesn't pay their subscription their store is disabled (so you get the 'store unavailable at the moment) message when you visit it but their products are still displayed on the home site.
We would have thought a shop that is disabled due to non-payment would not have it's products shown on the home site.