I don't believe Laporta had told Alemany that he had to leave the club. We didn't want him to leave back in May and were happy that he changed his mind, right? Also, Deco's incorporation has been long time coming, Alemany and everyone saw it and expected it, it is not a surprise.
What I don't know is what exactly Alemany's role sporting-wise is. I know he handles negotiations, but does he actually have an input on which players we should get and get rid of etc. like Xavi and Deco do? If his role is limited to negotiating with players and potential transfer targets, I don't see why he has to leave the club. And now he is going to leave, who do we have to handle that part of the process? I don't think Deco will.