Sorry, the splits don't tell the whole story here. Kimetto did not even try to sprint, so clearly, he had more to gain by coming second than by winning.
I know "team orders" exist in other sports, and to be honest, you cannot blame the two for using the rules to their advantage, if that much money is on the line. But clearly, the rules have to change for the future. In motor racing, you may benefit from your team mate letting you past to take the win, but at least you still have to beat the other contenders - that's not true in Marathon racing, where the competitors are in different races. I don't know about Mutai's contract, but it may well have had a clause of "no Makau" in it (he is running in Frankfurt this year) - and even if that hasn't yet happened, today's example would set a very bad precedent for the future.
I did not expect it to play out like this, but it was not difficult to predict Mutai to run for the WMM money first of all:
http://www.letsrun.com/forum/flat_read.php?thread=4826885
A simple solution would be to significantly decrease the WMM money relative to prize money for individual races, but perhaps a more elegant solution is possible as well.