Even though the arrangement would be based on direct booking and direct payment with listed hotel, the hotel needs to pay comission, sales incentive, whatever you want to call it, to organizing party, just to get to the list. Part of the agreed comissions can be collected in form of free rooms or other services in hotel.
That above described method of using central booking source for bookings, pre-charging the rooms and actually having lower net-net price level with the hotel is regular method used by many hotel aggregators.
All these are very common practises in business when we are talking about conference hotel booking arrangements or allotment based hotel room procurement.
CP