That just leads to it being used more and more and more in the future, and is not the solution to any problem.
Likewise, if Massa was taken out, he would unjustly have been denied the chance to fight for the championship. Regardless of its now-farcical nature, officially he is still in a position to be world champion. If he had actually asked the FIA to penalise Hamilton at Spa and Fuji then yeah, I'd see you point as a little more fair, but I don't think that he did make those requests, and so it's not actually his own fault that Hamilton has been hindered.
It may not be Massa's fault the FIA hindered Hamilton, but that's beside the point. As things are, without FIA intervention, Hamilton would already have been world champion. Massa should, therefore, count himself lucky that he still has a chance of officially becoming champion.
If Massa was taken out of the race, it would be unjust, granted. The consequences of this unjust act would, however, be minor; for it would be an even greater injustice that he was crowned champion at Hamilton's expense.
As I said before, I don't want to see the battle for the championship end in such way; but it would be a travesty of justice not see Hamilton as champion this season. Being Formula One world champion is the highest honour in motorsport and chances to win this title aren't usually around the corner, as it were, so it's vital that the person who wins the title is the just champion - not a false champion, manufactured by the FIA.

Ayrton Senna: WDC 1988,
1989, 1990, 1991
McLaren: WCC 1974, 1984, 1985, 1988, 1989, 1990, 1991, 1998,
1999, 2007McLaren: WDC 1974, 1976, 1984, 1985, 1986, 1988, 1989, 1990, 1991, 1998, 1999, 2008