Correct call for missed base?

[Mike Follett]

The umpire is not to call a runner out for missing a base(or to call DEAD BALL for that matter), if there is no appeal by the defense. This is the same for LL and ASA.
He pretty much screwed this one up, all the way around. The offensive manager certainly could/should have protested the call, as it was not a judgement call.
I agree, too, that I would have probably awarded the BR 3rd base, based on your description of the events, as I'd have ruled obstruction on the 2nd baseman, as well.