I'm not a TD, I just play one in a pub league.
I agree that, even if the BB didn't ask if the all-in player wants a call, folding to such a small raise is soft play. It's also extremely bad strategy, particularly with the ICM chop coming so soon. The chance to eliminate one player right before the chop? I'd take that chance every day of the week.
While a penalty, or even a warning, at that late stage would be pointless, merely explaining the situation while payouts are being made would probably be sufficient. However, I suspect that the player either figured it out or had it pointed out to him by some of the other players.
On the other hand, just how friendly was this group? Folding there is much akin to players agreeing to pay the bubble.