The FBI collects the private data of thousands of people they are innocent every time they use a mass-intercept warrant on a particular cell phone tower.
An attorney general collects the business records of thousands of people they know are innocent of wrongdoing in the course of routine investigations into fraud by large businesses.
Both of those are still considered "due process" because in both cases they are following a set process. Due process doesn't mean the government won't look at you if you're innocent, which seems to be a big misconception. It essentially means that the government should handle cases with similar particulars in similar ways.
So in the case of the NSA, if that collection happened under the same type of legal authority, after going through the same FISC review (if needed), was held to the same standards of reasonable and articulable suspicion (or whatever standards were required to be met for §215) then the collection that would happen from there would have been given due process.
As for your link, while its accusations are damning enough, they don't appear to support your first point or your last one. It's hard to argue DoJ is "ignoring" the law when the EFF themselves make quite clear that "The language of Section 215 allows for secret court orders to collect 'tangible things' that could be relevant to a government investigation – a far lower threshold and more expansive reach than a warrant based on probable cause. The list of possible 'tangible things' the government can obtain is seemingly limitless, and could include everything from driver’s license records to Internet browsing patterns."
