You are right with that. But that is just one side of it. Müller never made a secret out of it that he might leave when he does not see a good perspective for him. The question just is if that time has already arrived and what does the club do when he really would decide on leaving. His agent is not the usual agent - maybe that should be added, too. He is an ex-Bayern-player which Uli Hoeneß took under his feathers when he first arrived in Munich and did all the financial stuff for him and he is an ex-teammate of Sammer in Stuttgart. He will not stir up turmoil in the Bayern camp or outside if not necessary. One thing is about sure - Müller is atleast thinking about leaving - else they would have cut the rumours short very fast as there are no contract dealings. That they do not is showing.
The club - that is a two-sided-sword. The fans already started to whistle when he was subbed in the Real Madrid match and started to sing his name - and he like everybody else was not playing well. You can predict turmoil if he stays - and there will be if he leaves. That nobody wants him to leave not even Guardiola is very clear. And he is somewhat their mascot and the one most featured. But to prolong with everybody, to maybe keep Mandzukic, the acquisation of Götze and Lewandowski etc. and especially Pep and his system do not help a player like him who is so versatile but does not have a clear position and that can backfire.
well probably go in for Strootman which would be a more mobile option of not as exciting.