My take on the situation is that both teams are being recalcitrant towards coming back onto the field of play - not just Team B.
I like Jason's solution to this problem. Make the ball ready-for-play. This will force Team A to come out. If they don't, flag them for delay when the play clock expires. When Team A arrives, the U should go over the ball and prevent the snap. If Team B does not match up (come onto the field of play), charge them with delay of game.
^^^ This.
Nothing complicated here. I've had an offence delay coming out to the field. I blew RFP and waited for the clock to wind down. Problem solved: they only did that once.