12 players on the field

[tmunz]

I was wondering about the following situation: Team A trips a player from Team B in the penalty box. The ref awards a pk. Prior to the pk the linesman tells the ref Team B has 12 players on the field. The ref books one of Team B players and then allows them to take the pk. Shouldn't Team A be awarded and indirect kick at the spot the where play was stopped? Should Team B still be allowed to take the penalty kick. You are basically rewarding Team B a goal for having 12 players on the field.

Thanks