No. Under no circumstances is it acceptable for governments to ID readers of a news article. Such an act is a direct attack on the freedom of speech, freedom of thought, and freedom of the press. IMO it very clearly crosses a line on what law enforcement can and cannot do in a democratic society.
Note that law enforcement has (over)broad powers for investigation at their disposal already, and they were able to find the suspect "through other means." There was no justification whatsoever for the subpoena.
The danger comes when law enforcement uses the evidence they gather from one case, to target someone who hasn’t committed a crime. Which clearly hasn’t been shown to be done here.
Media, news and journalists and their sources have special protections and consideration that random private club does not.