On F9 flight 6, the first demo of the V1.1 configuration, the putative rationale for the extra second stage burn was to demonstrate relight capabilities for Geosync, and really, any orbit that requires more than one burn to achieve.
But one thing Elon Musk said in his press conference after the flight has me wondering. (I cannot find a link to a transcript).
He described the burn they attempted on the second stage as "sideways".
If they were really trying to demo relight for a GeoSync launch profile, you would expect a more representative burn attempt, which would be generally to a higher orbit, and probably not described as sideways.
But if they were going to take a shot at de-orbiting the second stage, just to get some data on it, a sideways burn to slow down would make some sense.