The government does not require companies to comply with a scheme. Companies are free to contract with the government, but certainly aren't forced. PRISM & Muslim registries are also edge cases. There are many companies who choose not to do any work with the military, defense industry, or even gun, drug, or tobacco companies for ethical reasons. Most companies will allow their employees to opt not to work on projects that violate their ethics or values. However, a company would certainly be within their rights to fire an employee for refusing to participate in a project. (its not a smart move, nor does it help with retention of other employees) None of this is, by any means, civil disobedience--nor are ethics and civil disobedience interchangeable. (& it doesn't have to be illegal to be unethical--but civil disobedience is about law-breaking.)
As you may remember, the courts would not permit the government to force Apple to build decryption software to crack that iphone.
And we should not welcome all or encourage civil disobedience. We should just create just laws. Also, we should not redefine or expand the definition of civil disobedience.
Civil disobedience is not a "sentencing consideration." All of this is so inside baseball that it'd take explaining all of civil & criminal procedure in order for you to understand. It would take me a long time to make it both clear and accurate and the payoff would not be worth it. Sorry, but yes, you are making many mistaken assumptions:)
There are many public policy reasons why corporations do not & are not considered to engage in civil disobedience. Here's a few quick ones: we don't want companies to direct their employees to break the law or ignore health safety or environmental regulations, or to encourage the formation of criminal enterprises, most (99%?) are defined by a profit-making purpose & this undermines that (& create shareholder lawsuits.) and, despite Citizens United, the overwhelming majority of our laws do not treat corporations as people. For instance, corporations, legally speaking, are not considered to have mens rea or intentions.
TLDR: Citizens United aside, it is actually just not useful or accurate to consider corporations as people, because they aren't. As far as our legal system goes, humans have intentions & a state of mind and corporations don't.
(Feel argue they do, but, as far as the US legal system goes, they don't. And shouldn't. Because they actually don't. So, please, don't. Or, just don't expect my response).