What Villku92 said.

As a general rule, if you see a fully damaged government or barracks building in one of your towns (including ones you've just conquered), and there's been no rioting or enemy sabotage to cause that damage, then it's very likely that the damage should be viewed as an instruction to you from the EB script to destroy that building, because it's either foreign to your faction and should not exist in your town, or it's outdated and no longer required because there has been a military reform since the building was built.

Destroy the building immediately.