I can't really think of any advantages for keeping a player against his will.
The world of football today is not dictated by the teams anymore but moreso players and agents. Take Raiola for example. If Milan alienates him from the club, they lose dramatically. If we take even 1 or 2 of Raiola's young, promising clients that would have otherwise wound up at Milan, we come out miles ahead.
It's a disgusting reality, but it is reality. Marotta knows this very well. He doesn't burn bridges with any players or agents. As long as we are seen as a favourable destination, for whatever circumstance (even as a stepping stone), then we will ultimately profit in the end sporting wise or financially.
Even in this scenario with Alves. We got him for free, he almost propelled us to the CL. And we lost him for free. In the end, as always, we come out with a net positive. Now if we hold him hostage, maybe we squeeze out one more year of him actually trying. But the risks are numerous and way more damaging.