On a multisite there's no "Free level" (no "Free signup" allowed) and two levels. The customer selects one of the Pro Sites packages and the site is created based on the default "blog template" (via New Blog Templates plugin).
Let's say that there's a "Basic" and "Vip" package. For "VIP" level all the plugins are avilable. For "Basic" some are not and that's taken care of by Pro Sites via Premium Plugin Manager.
However, some links on the "Basic" site must be hidden from front-end too. How to do it, given that it's the same default "blog template" etc?