Interesting Time-Out Situation

This came up the other night at our association meeting (NFHS).

Team A calls time-out. Both teams go to their respective sidelines for an authorized conference. At end of time-out, Team A comes out and lines up, ready to run a play. Team B continues their conference on sideline with their coach.

Question that came up: Do you as referee mark ball ready for play and allow Team A to run an "uncontested" play? Or do you assess Team B with a penalty?