Alonso was running ahead of Massa in the dying moments of the session. When Alonso crossed the line to start his second flying lap he only had two seconds to spare before the end of qualifying. Massa was completing his lap. Had Alonso backed off, there is no question that Alonso would not have been able to set a time.
The penalty regarding the rules may have been correctly enforced regarding Massa. But had Alonso obeyed the rule he would have compromised his own qualifying session, when it was Massa’s fault that he was stuck behind Alonso on the track to begin with.
It’s very disappointing that such a contentious ruling has affected the championship battle so severely.