The reigning champions cruised to a comfortable 4-1 victory after their opponents were reduced to 10 men, but Marotta would have preferred to bag the three points against a full Zebrette outfit.
"The goalkeeper's red card was a big factor in the game and I honestly think it was a harsh decision," Marotta was quoted as saying on the official Juventus website.
"We came to the Friuli for a win. However, winning against 10 men is no great joy. We would have preferred to beat them on equal terms. We're pleased to have won but would have preferred to do it against a full team.
"In the next meetings we'll have to start a dialogue with the refereeing body with a view to changing this rule or getting referees to change their approach, because this damages the game as a spectacle."
Juventus resume match action on September 16 away against Genoa.