There are three slightly distinct issues here:
1) Fuglsang criticised the team and team management in public.
2) Fuglsang spoke to the media about looking for another team outside of the transfer window.
3) Fuglsang, because he is leaving, will score points for another team rather than his current one.
(1) is not really all that relevant here, although it won't have predisposed his team to kindness over the other two issues. (2) Would get you in major trouble at, say for instance, a football club and might well get you benched. (3) Is a result of an idiotic system unique to cycling which actually makes it rational to bench one of your athletes in favour of one who he might have the edge over on sporting criteria alone.
I bow to few in my lack of sympathy for Bruyneel, but while you can and should blame team management for the deteriorating situation inside the team which leads riders like Fuglsang to want to leave, it's difficult to argue that Bruyneel is being irrational in his response to that statement. Once it's gone that far, from Bruyneel's point of view, the rider is a liability rather than an asset.