Bonucci this month joined Milan in a stunning transfer that served as the marquee move in a busy transfer window at San Siro.
The Italy centre-back has claimed that being banished to the stands for a Champions League game with Porto was "the last straw" as his relationship with the club and coach Massimiliano Allegri broke down.
But Marotta offered a different explanation, telling Sky Sport Italia: "With Bonucci we accepted his personal and professional desire, which was to join Milan.
"There was the feeling he could go. It was not about incidents so much as motivation that was lacking.
"We have found that keeping players against their will is counterproductive.
"An individual has left, a champion, but many others have remained and there are some talented young players already in place. We made calculated risks.
"I am confident, as we have a group of very strong defenders. And like Bonucci joined us from Bari and became a great player with Juventus, we have some interesting young players ready to do the same."