How so Ferrari have always maintained that the WCC is more important it wasn't until the Schumacher era that they were perfectly fine with making sure whoever the star was, that he too was happy and got his way. Now that's not to say Ferrari haven't always made sure things when the way they've said, but MS driving for them was probably the first of many drivers to be made sure he got his way so long as he was leading the Driver championship.
If Ferrari truely are invested at staying at the top or even winning again on a champion level then the second driver gaining extra points a couple times over the main driver shouldn't be an issue. Especially if they believe they can give Vettel the same thing he had at RBR.
But as can be seen at Merc, obviously the lesser driver taking away from the first place driver doesn't hurt anything.