Disqualified player question...

[Sirrefalot]

Newer official here, third year. Player a1 picks up 5th foul. Teams are lined up to shoot free throws when horn sounds and score table informs officials that it is the 5th foul on a1. Official notifies coach, and player and instructs table to begin 30 second clock. Player a1 runs off court, gets drink and sits down (all the while the coach is in a stare down at me). Question is, does it matter that the player left the court? he called his players over for a time out and insisted that he had a minute (even though i told him 30 seconds). Should i be concerned about anything other than he should have his player in before the 30 seconds?