Mackail-Smith will miss the Carling Cup visit of Gillingham on Tuesday to link up with the Scotland squad for their Hampden Park clash the following day.
"We will always respect players who want to play for their countries so we won't stop him from going," Poyet told The Argus. "Saying that, it's not very clever when you put an international game in the middle of a week when you have a cup game.
"This is Scotland, not Australia or Argentina. I think they knew from two months ago that it was a Carling Cup week and there are a few Scottish players in England.
"I am not going to fight the Scottish FA over it. I am going to give him the freedom to go. I loved playing for Uruguay. I will never stop a player playing for their national team.
"I am very pleased for Craig and I would, of course, like him to play. It would be very disappointing if he goes to Scotland, misses the Gillingham game and doesn't play, so it's up to the manager."