I still firmly believe he put Rubens on a three-stop strategy to ensure Button would win. Not out of nationalism or favoritism, but because he knows who is the stronger driver and with Button only getting half-points in Malaysia, they need to make sure he maximizes points because the RBR look(ed) like a threat.
If Malaysia had been full points, I think he could have afforded to let Rubens win. But with the last two championships decided by one point, two points were too much to risk at that stage of the game.
I don't think he was put on a 3 stop - he started with the same amount of fuel as Webber.
One of the problems Rubens (and Vettel) have at the moment is their tyre wear. IMHO one of the factors behind Button's success has been his ability to manage the option - I think Barrichello's problems in this department have caused Brawn to worry about this and thus have given themselves the option to change him to a 3 stop if necessary. Rubens also seems to prefer running on a lower fuel load.