Pastor,
I think there are times that the correct, by the book rules, can not be applied. This is one of those situations. There were multiple mistakes made by all...the bettor, the silent all-in raiser, and the dealer.
I also want to mention the use of the all-in button. I originally thought it was a great idea, and when used properly it is. However, in the situation you described, it is ineffective because the dealer was (obviously) unaware Player B was all-in. So the All-In Button would not have been used... Correct?
I believe, in the best interest of the game, the proper board cards must remain and the uncalled portion returned to the silent all-in raiser. I said it before, and I'll say it again, there is no way to ask Player A (if he was the loser) to add more chips to the pot, or award him the "extra" all-in amount, if he were the winner. Too much action has transpired. The time to draw attention to any irregularity is certainly before substantial action has occurred. In your scenario, two betting rounds and the showdown commenced before the mistake were noticed.
One other note: You mentioned using the 50% rule. That would certainly simplify things, wouldn't it? The problem that currently exists (because there is no % rule in NL or Pot Limit), the amount of the unnoticed all-in could be anything. It could require less than 10% or 10 times more than the the amount wagered. It shouldn't make a difference, under current rules, but we all know, it could make a huge difference in the outcome of the hand, and the tournament.