I agree that what Microsoft is saying is bullshit, because when push comes to shove in any case they will have no choice but to balk with their challenge. However, there is a very twisted image of the results of the data collection, including but not limited to how the data is screened, analyzed, and resulting action. This isn't anything like the device in The Dark Knight or Person of Interest, nor is it someone being able to hit a couple of keys and access your Skype video or key into your party chat on a whim or over a couple of words hit on a screening of the data.
(There have been wiretaps in place, but over the years things have become far more focused on thinning out the data rather than mere interceptions, as demonstrated in the fantastic article from Freki. Wiretaps and signal interceptions are typically further down the line, though as always individuals within a system can and will abuse it if they are that type of individual without the proper oversight.)
If, and it is possible given what we saw with the TSA employees, a person does somehow circumvent all the red tape to spy on a random individual, that is the issue of the individual, not the overall system in place.
Not trying to offend anyone or support the NSA (Too poor of an execution to do both in clarity by all definitions and the execution of the system), but it's hard for us to be seen as having legitimate complaints when their directed towards a fantasy image rather than the far more boring reality of a bunch of servers and paperwork.
Finally, yes, it does set a bad precedent with no positives in sight given how there haven't been any public (if any) claims on the system in place preventing or following up successfully on a threat to the U.S. or their environment of laws. Not going to argue there. Just wish that people would focus more on the direct issues with the system rather than focusing on the more fantastical/improbable/outlier elements.