We have absolutely no idea what goes on behind the scenes and even though it's fun and mysterious to pretend the MLS is out on some personal vendetta, it's just not practical.
Also don't lose sight of the fact that Gilberto is absolutely worthless with respect to world football. He's a dime a dozen striker without a left foot that's seeing his potential vanish more and more as the days go by. Outside of Portugal, I'm not convinced he'd be wanted anywhere in Europe.
Who cares where he goes, it's pocket change to MLSE.