The problem is that all that information already exists. Google and Facebook know everyone's religion (and ethnicity and so forth). And as Snowden revealed, the government can get access to those databases.
And you can be sure they already do so specifically for Muslim people, for terrorism intel purposes.
If the author of the piece were serious, we would need to start by getting Google and Facebook to remove that information. Or stop working with the government. Or stop working at those companies until they do. But the author realizes that is something people wouldn't accept, I guess, and suggests we "not help create a new database" which just a meaningless distraction.
That said, it certainly behooves Facebook and Google to be thoughtful about what data they keep in a form easily accessible to the government.
The only option is for Google and Facebook to not have that information in the first place. That's just not going to happen - there is tons of financial value in knowing people's religion, ethnicity, etc. etc.
1) Donald Trump has called for keeping a database of Muslims, to surveil and police them. Do you recognize the truth of this statement?
2) Is it bad and oppressive to target a stigmatized minority religious group for government surveillance and policing?
3) Are software engineers morally obligated to not implement oppressive policies? Or is whatever they do justified, so long as it came as an order from above?