I was under the impression that Pro Sites and MarketPress got some new functionality when Pro Sites was released, it wasn't what I thought was going to happen but maybe we can get this on the roadmap since it would be a useful tool.
I want to offer two Pro Sites levels (call them Basic and Pro). The basic level gives auto-activated access to MP and the seller is forced to use PayPal Chained payments and I get a commission on each of their sales (and the monthly rate is low). However, for professional-level sellers who might have higher volumes this commisssion will eat into finely-tuned margins so I'd like to be able to offer a Pro-level account with a significantly higher monthly fee and then give them access to the additional MP payment gateways (Authorize.net, etc.) so they can avoid commissions and only pay a fixed subscription fee to take advantage of selling on my network.
I think the fix here is for MarketPress to recognize the Pro Sites levels so that when multisite owners are configuring the payment gatreway and theme permissions on the MP multisite configuration page we have more fine-grained control over what we can offer.