Did I read that right? you had a chance to triple up with the 2nd best hand in poker and didn't go for it?
Yes the BB's hand is scary, because he put himself in a position where he can't be bluffing, but I think you have to go for it here. Some people will tend to overplay jacks or queens like that, and in this case, the hands were even worse than that.
In a cash game yes, tournament though? Really really tough, but you would probably want to lay it, as hard as it may be especially if it's really early in a tournament.