Hmm, sorry, but civil liberties come first. Companies don't think for themselves, although they are technically individuals under the law.
In some cases, it's a matter of giving up both liberty and security for the economic liberty of others. I suppose you could call that greed.
The thing about the "it's law and they should follow it" is that it's really not that great a stance. Laws are not the end-all be-all. They should be followed, but should not be something to follow for the sake of following. First and foremost laws are there to protect the people...whether it's all people, or just a certain group.
The problem comes when laws are used to benefit rather than to protect. Is a law protecting profits, or is it protecting rights? Saying that a company should be getting a certain amount of profits in a free market system is a very slippery slope; and at this point, the US isn't really a free market. In fact the current system is very monopolistic. What with the widespread ownership of 'ideas', it's very difficult to do anything because you might 'infringe' on someone's 'rights'. You put double-clicking in a program? Oh, that's owned by Microsoft. Your product is illegal.
Money used to be a form of compensation, now it's basically a transferrance of power.
In this case, I suspect that the full system scan will only be used to generate internal lists and statistics on software piracy by Microsoft. If they start suing any of these people, their plan to get them to rat out the distributors will fall apart. Keep in mind that software piraters are going to be some of the more well-informed computer users out there; if any legal cases relevant start to happen, they're more likely to know.
When it comes down to civil rights vs economic rights, you do need some economic rights to live enjoyably, but not as many as civil rights. And if you give too many economic rights, you end up with people 'bettering themselves' by just getting richer and richer. Maybe it's just me, but I think it's more important that one be allowed to be free of discrimination than to be forced to have less than 27 billion dollars in the bank. (Well, at that point, you'd probably be able to fund a regiment of the USM to build a military base around a heavily guarded vault)