Yes, non-violent political activists, such as the nun that broke into the Oak Ridge Nuclear facility, should receive jail time, because they pose security issues for the rest of us. She can find a way to make her point that does not endanger national security. When she was breaking in, people did not know that she did not intend harm.
The woman's status as a nun does not nullify the justice system. Regardless of her motivations, she still broke the law. If anyone else broke into that facility for any other reason, no one would question whether they should go to jail. The law is very clear. If you break the law, you should be punished.
Those who do not just stand outside a facility they are protesting but actively break and enter or destroy property know what they are doing. I admire them, but I do think that going to jail for a brief period of time is something that needs to happen because it takes a lot of courage and they know it will happen.
Yes, if they break the law in ways such as breaking and entering, political activists should get jail time - even if they aren't violent. Things such as breaking and entering and vandalism cost people money and does damage to property. Everyone has a reason they did what they did, but that doesn't mean it isn't still against the law.
Non-violent political protest is the cornerstone of our democracy. Activists like Martin Luther King, Jr. used civil disobedience to bring about the end of the Jim Crow South. Judges and juries should take political protest into account when sentencing individuals like the nun that broke into Oak Ridge Nuclear facility, and they should not be put in prison.