I've seen no price different when comparing booking thru or seperate. The problem for me is none of the fights Disney offers are nonstop.
If I book thru Disney I get offered Delta or American with transfers in Cinci., Dallas, Chi., or a couple other cities. If I book with SouthWestAirlines I get at least 4-6 nonstop there and 6-8 nonstops on the way back. So for me it is a choice of 2hrs15min (nonstop) VS. 4hrs25min-6hrs50min changing planes.