There is most likely some truth in that, but that would be dumb from the teams perspective, Its better having both your drivers on the podium than one. If I remember correctly Barrichello did do well in a Ferrari. How many Ferrari 1-2's were there?
Yes the teams no 1 drivers gets preference in terms of strategy but when it comes down to the cars both would be on the same level, minus the set up the driver prefers. Not all drivers are equal, if you look at the telemetry is clear as day light, unfortunately we aren't privy to that information.
As for Alonso, he had a hand in his own demise at McLaren. (Not saying McLaren want also at fault)
Here's an interesting video about Michael and his driving style VS some of the guys he faced in his early days
http://www.youtube.com/watch?v=Uk2p2nRK-p4
The same might be true for Vettel and Hamilton VS the rest and even between each other, but we'll never know