Two late Stoke goals inflicted a 2-1 loss and added to the disappointment of MacDonald who has turned down the chance to become Gerard Houllier's assistant boss.
And the Scottish coach admits he has a decision to make over whether he returns to Villa's reserves or seeks a management position elsewhere.
"I put my name in for the job and once I did that I knew I'd be disappointed if I didn't get it," said MacDonald.
"I've got a decision on whether to go back to the reserves, I need to re-evaluate that. I'm doing things for me."