2 points:
1) Bonucci is one of the best passers when it comes to defenders. We will lose that without him, Chiellini and Benatia will just hoof the ball. Barzagli is declining, Rugani will have to start instantly and Caldara potentially too if Barzagli decline or leave in summer. Huge change at the back, lets add that we might add Verratti for Khedira and Di Maria for Cuadrado. Seems a lot of change, i can see a difficult start where not all settle in, remember 2 years ago.
2) Even if for a longer term, selling Bonucci right now would bring a negative message. Selling another major star (sold Vidal and Pogba previous summers, selling Bonucci now, is Dybala gonna go next year?), like i already said Barcelona, Bayern and Real dont sell their key names/players who start regularly unless there is personal reasons (Kroos wanted new challenge, left for Real).