This is a really interesting question! The Guard marker gives the creature's quick melee attacks counterstrike. The steps of an attack is where we find the answer to this. Since the damage and effects step (or roll dice with Academy) happens before the counter attack step, the Stagger would be applied before the counter attack step. During the counter attack step you check to see if the defender has the counter attack trait on any of its attacks, since it lost it's guard mid attack it also loses the counter attack trait on it's quick melee attack.
tl;dr -> the minor creature loses it's counter attack.
