All governments pursue a limited number of the charges that can be pursued. That our government like all other governments also pursues a limited number of cases does not make it illegitimate.
There is no power given to the federal government to use terrorism. Acts of terrorism committed by federal executive officials are not those of the government, but rather those of the executive officials, individually or severally. That is why those officials can be prosecuted. Such acts do not impact or affect the legitimacy of the federal government.
By contrast, illegal acts by a state government, passed by the legislature, and ratified by the governor can remove legitimacy from the state government. Illegal acts passed by a convention of the people, elected for that purpose, can do the same thing.
Wow - You are utterly off base. Just because the act is illegitimate does not mean the act cannot be done.
Your view of the government means that the government literally cannot do any wrong. It is very close to elevating the government to the position of God.