Note there must be "intent to injure, interfere with, or obstruct the national defense of the United States." I don't think this nun's intention was injury, interference or obstruction. Her actions were highly symbolic: Splashing human blood, spray painting a Biblical verse, and defacing a building.
In any case, there is no "right to protest." The first amendment only guarantees free speech, press, assembly, and petition for grievances. And even these "freedoms" are quite limited. OWS got tear gassed, billy clubbed and shot in the face with teargas canisters and rubber bullets for trying to exercise them.
Christians have been willing to suffer this kind of persecution, go to jail, and even die for their beliefs, ever since Jesus set the example for them.
Tougher laws and harsher sentences doesn't stop protest. The protests raging in Kiev right now were started by a new, tough anti-protest law.
In my opinion, the nun should have been charged with trespassing, tampering and vandalism (36 CFR 1002.31). Overcharging with sabotage and terrorism really just shows prosecutorial vindictiveness. Just laws and punishments are proportional to the crime.
> bypassing armed guards
Sounds like the guards should lose their jobs. The security contractor should lose their contract, and maybe pay the taxpayers back whatever they were paid. They clearly failed their mission in every conceivable way. What if this had been a real terrorist instead of an 84-year old nun with a can of spraypaint, some blood and a hammer?