It read like a privacy issue. Then I read your comment, and was confused.
> More proper would be "NYPD Bypassed Facial Recognition Ban to ID Rock-Throwing Assailant"
This is inaccurate. The charges were dismissed. At best, it's an alleged rock-throwing assailant.
> In the end, this is not a free speech issue except tangentially; it is a privacy issue.
That's what the original headline suggested to me on first reading. Why did you think the headline was a free speech issue?
That being said, the threat of a government disobeying its own rules and policies is a deterrent to free speech.
It provides context. The US has an extensive history of illegal/unconstitutional/questionable surveillance of protesters. This could be seen as either another example of exactly that or, at the very least, as a warning that the police in NY are willing to illegally use facial recognition when it suits their interests.