Because for the rest of the race, Alonso will have tyres that are four laps fresher than Vettel. Ferrari left it as late as they could. Webber right there with Alonso.
I don't think Ferrari could've done anything about Vettel, but giving Alonso fresher tyres will be a big advantage if there's a safety car.
I don't think 4 laps' freshness will make much of a difference for the hard tyres, especially given it puts Alonso 3-4 seconds behind Vettel. Unless there's a safety car, which is unlikely because the Monza stewards tend to be very good and there are lots of run-off areas, I suppose Ferrari have to roll the dice though.
Hamilton did a great job...if he didnt have that tyre problem he would have been fighting for 4th or so.