User blog comment:IamJakuhoRaikoben/Chapter 440: God Serena, Review./@comment-4449950-20150615065859/@comment-76.161.172.226-20150615161530

Makarov's actions make some sense. Albareth clearly knows that Fairy Tail is in possession of Lumen Histoire. The guild together would be a primary target for the empire. If for no other reason than to remove them as potential protectors of it. Disbanded on the other hand, the empire has little reason to go after it's former members. They're all scattered about, and the empire has little reason to think they know anything about Lumen Histoire. Instead of Fairy Tail being a target, it's just one more already removed obstacle like the deceased council.