Aren't you also ignoring, though, the whole "Whelan simply does not know that the ball is not supposed to be snapped" part of the equation, because he never practiced the play, even once?
I'll assume that Pagano called for the play.
The ST coach should then have said "Coach, we lost the snapper. This personnel hasn't practiced it". Did he? If not, be bears lots of the resposibility.
But Pagano should also have asked his ST coach, before calling the play, "are we ready to run this one?"
Just like Josh McD asked Edelman, before his big TD pass vs. the Ravens, if he was ready for that play to be called. You've got to make sure than you're on the same page, when calling something THAT unorthodox, as McDaniels was, and (presumably) as Pagano was.
The McDaniels thing helps the Pagano defense. That's not BB (HC) asking. That's the OC (ST equivalent in the given scenario).
According to McAfee:
Whelan practiced with the punters during the week
Whelan was fielding punts when the change about drawing the opponent offsides was put in, so he didn't hear about it
Usual 'center' was injured in the 2nd quarter of the Patriots game
Whelan took the place of the 'center', and assumed hands under ass meant he was to snap the ball
Hilarity ensued
What we know from TV:
After all hell broke loose, Pagano asked why the ball was snapped
So, from a combination of the above, and for purposes of people saying he should have called the TO because of the players not being lined up correctly, we should be able to safely assume that Pagano didn't expect the ball would be snapped, and a simple DOG penalty would be his expected worst case scenario.
From your McDaniels/Edelman reference:
It would be the ST coach that should be telling the snapper what to do and/or not do, just as it was McDaniels talking with Edelman. The ST should either have made sure that was dealt with, or he should have told Pagano that the play couldn't be run.
One can easily make the argument that the ST coach blew it three times:
Failing to tell Whelan during the week
Failing to tell Whelan during the game
Failing to call off the play because of the injury/replacement situation
Transferring that to the HC by any means beyond "final responsibility", though, is a different issue entirely.