Poker Ruling

So, the BG and I were talking about his post on oddjack, and while browsing OJ (which I only do when BG tells me to: I'm not exactly their target audience), I notice a link to the following article: More Raising in No-Limit Hold’em - You make the call in a no-limit hold’em betting situation on the river

The situation:

The game was $2-$5 blinds no-limit hold’em, and the situation took place on the river with only two players in the hand, Player A and Player B.

The dealer explained it to me this way:

Player A made a motion with his hand that resembled a check. The dealer didn’t hear anything from Player A, so he moved the action along to Player B, who made a bet of $100. Player A threw his hand faceup on the table. The dealer assumed this was a fold, so he took the hand and put it into the muck. Player A yelled to the dealer, "Wait a minute, I bet all in."

Player A explained it to me this way:

He announced "all in" on the river, Player B moved his stack in, and Player A took that action as a call and put his hand faceup on the table. When the dealer mucked his hand without the other player turning his hand up, Player A knew there was a problem.

Player B explained that he also saw what appeared to be a check on the river by Player A. So, he made a $100 bet because Player A checked.

A few other observations from players at the table were as follows:

The player next to Player A said he heard him say "all in." No one else at the table heard him say anything.

A player in the middle of the table said Player A immediately responded when the dealer mucked his hand.

Another player said that Player A tossed his hand in faceup (he took that as a fold, because he didn’t hear Player A say "all in"), and when the dealer mucked the hand, Player B made a motion to muck his hand, which he assumed Player A took to be weakness. It was only at that point (Player A sensing weakness) that Player A said something.

There was total consensus that Player A held 10-9 suited, as everyone saw it faceup on the table. The board read 9-6-3-J-J. Player B’s hand at this point had not been revealed.

How would you rule?

I'm of two minds of this: the first is that the dealer took the action as a check and the cards are in the muck, too bad so sad player A. However, there was someone at the table who did hear player A's 'all-in'. So, I think I rule in the following manner:

Player B's bet of $100 stands. Action is on Player A, he can call the bet, fold, or raise - all while knowing that Player B is aware of his cards. I'm waffiling a little on the raise part, but since Player B knows the cards, if player A raises, he knows if he's going to get beaten or not, so seems like an okay thing to allow.