The Australian striker scored two goals - in the 15th and 73rd minutes - but Boro were pegged back both times as Ludovic Sylvestre (21st minute) and Jonjo Shelvey (78th) netted for the visiting Seasiders.
Mowbray subbed McDonald for youngster Bart Ogbeche in the 83rd minute and the former Celtic man was clearly unhappy at being hooked but the Teessiders boss feels he was right to make the change.
"You could argue that I haven't been happy for the 13 or 14 games that he didn't score!" Mowbray told the club's official website.
"But it's a passionate game and my job is to try to keep him hungry, not to keep him happy. It's the team that matters and as long as he's hungry to score another goal next week then that's fine."