If they don't want massa to win they shouldn't enter him
The job of the No.1 driver is to take the risks and bring home the WDC (assuming the car is good enough).
The job of the No.2 driver is to bring in good points and to assist the team to win the WCC (to expect the No.1 driver to win the WCC on his own is asking too much). There is less pressure on the No2 to win, but more pressure on him to make less mistakes and bring the car home consistently.
The other job of the No.2 is to assist the No1, where necessary - we saw this happen on Sunday. Also, the No.2 driver might be asked to slow the rest of the field down to allow the No.1 to open up a gap. This is seldom seen. The best example of this that I can think of was when MSc broke his leg . He came back (1999 - Malaysia) and assisted Irvine. In this race, he allowed Irvine ahead of him and then backed up the pack behind him. In my memory, this is the only time when I have seen the No.2 driver (which is what MSc became) being able to successfully do this. Perhaps JRS can pull up some other examples?
Finally, should the No.1 driver drop out, all efforts from that point onwards are focussed on the No.2.
Just because Ferrari have a No.1/No.2 system in place, it doesnt mean they should only race with 1 car.
The No.1 and No.2 system has been in operation for many many years. In recent times we can look at MSc/Irvine/Barrichello/Massa at Ferrari. We can also look at Hakkinen/Coulthard/McLaren. We also saw the No.1/No.2 system in operation while Heikki was at McLaren (if Heikki was in front of Hamilton, Heikki would move out of Hamilton's way - I think we saw this in Germany 2008?). Heikki understood that he was the No.2 driver.
The problem we are seeing this year, from Webber (and to a lesser extent - Massa), is that some No.2 drivers don't want to accept their position and it is this which is causing problems within the team.