I agree with you the first part. The way I see it, the only thing that should've been done differently, is that the lapped cars (all of them) should've been allowed to overtake a lap earlier, when the no overtaking message was sent out. Going by the team radios it seems quite a lot were expecting it at the stage too. Sainz especially went on about wanting lapped cars to go. If all the lapped cars had overtaken at that point, which was roughly the same part of the track, the safety car would probably have to go for another lap and the race would still have re-started at the same point in the race, and you'd expect the outcome to be the same.
Masi, who would know the regulations better than most, stated that the purpose of Article 48.12 was to remove those lapped cars that would “interfere” in the racing between the leaders and that in his view Article 48.13 was the one that applied in this case. He also stated that it had long been agreed by all the Teams that where possible it was highly desirable for the race to end in a “green” condition (i.e. not under a Safety Car).
They should really limit the number of people allowed to talk to the race director though. Should probably not allow team bosses to do so, they're the ones that get most emotional. i.e. Wheatley is usually a lot calmer than Horner. 'I'm not sure we agree, but I understand' for instance, at the lap 1 incident.