1. This is very good for one reason: Iran. Flynn has been the strongest Iran hawk in team trump by far. Him being out greatly reduces the odds this happens
2. The intelligence community isn't good and is entirely self serving. Pretending they have any values outside of the continuation of their patronage and a vague commitment to American Empire is ludicrous and short sighted.
3. This is not the start of trumps fall. The IC will not move against trump because trump has no political commitments that infringe on their values per se. They might find it off putting that he admires Putin but as long as the checks cash and black sites get greenlit they aren't doing shyt to him.