This is self contradictory in my opinion....Alonso was being held up by Massa which was allowing Vettel to close the gap. If that continued, you'd have Alonso defending P2 to Vettel, and Massa would more than likely be involved in the fight as well, especially if Vettel found a way passed Alonso.
It's no different to being told to hold station. The only thing that made it worse is the way Massa went about letting Alonso through, obviously letting everyone know he wasn't happy about it.
At the end of the day, I believe Alonso could have challenged Massa for P1, but probably didn't want to repeat the RBR incident, and followed Massa until the team let Massa know Alonso was quicker than him.