Judge Richard Sinnott refused to dismiss charges against some counter-protesters of Saturday’s “straight pride” parade, despite calls for leniency from Suffolk County prosecutors.

Thirty-six people were arrested on Saturday, 34 counter-protesters and two people affiliated with the straight pride event. Charges ranged from disorderly conduct to unlawful possession of a weapon, according to the Boston Police Department.

At arraignment proceedings at Boston Municipal Court Tuesday, Sinnott denied motions filed by prosecutors to throw out charges against seven people, some facing disorderly conduct charges, and some facing charges of resisting arrest.

The judge’s refusal to drop the charges at the request of prosecutors drew criticism from District Attorney Rachael Rollins, the ACLU and others.

Rollins said in a statement issued Tuesday night that Sinnott “punished the exercise of individuals’ First Amendment right to protest” and said she would “use the legal process to remedy the judge’s overstepping of his role” for “those people now tangled in the criminal justice system for exercising their right to free speech.”

Prosecutors did move to arraign seven more individuals for charges including assault and battery on a police officer, carrying a dangerous weapon and accosting.

“Make no mistake: some people were appropriately arraigned and will be held accountable for actions that put the safety of the public and law enforcement at risk,” Rollins added.

Sinnott ultimately agreed to drop charges against two of the 16 protesters who came to the first arraignment proceedings. Defendants who were arraigned on Tuesday are expected to return to court later this month, and in October and November.

Five more people were held on bails ranging from $100 to $750. Prosecutors argued that one woman should not be held on bail, after which Sinnott posted her $250 bail. One man was held without bail after being accused of disorderly conduct and resisting arrest. Several people were taken away in handcuffs.

Boston Patrolmen’s Association President Michael Leary says he was both pleased and surprised by Sinnott’s decision.

“The charges are serious, and I appreciate the judge ... not throwing them out of court,” he said. “I thought there'd be some dismissals and people walking out of court high-fiving each other, thinking they had a victory of some sort, but I was very happy with what happened today.”

But Matt Segal, an attorney with the ACLU, said he was baffled by the judge’s decision, describing it as “concerning.”

“If the commonwealth has no interest in the further prosecution of somebody or in the imprisonment of somebody, or somebody having to post bail, it's unclear why a judge would require that,” Segal said in a phone interview Tuesday. “If the commonwealth were saying, 'We would like this prosecution to be over,' or, 'We would like the sentence to be not that harsh,' and the judge goes beyond that, it's simply concerning.”

Northeastern professor and WGBH News Legal Analyst Daniel Medwed said Sinnott’s actions were “odd and disturbing.”

“It strikes me as unusual that a judge wouldn't go along with the prosecutor's recommendation like this,” he added.

During an event in Roxbury Tuesday night, Rep. Ayanna Pressley was asked to clarify her support for counter-protesters, after she retweeted a message with a bail fundraiser for those who had been arrested.

Pressley said she doesn’t support violence and called for further examination of the circumstances around the arrests.

"The footage that I have seen only leaves me with more questions,” Pressley told reporters. “That is why we need an independent investigation.”

Pressley said she is “grateful” for those who protested to affirm the city of Boston’s values and added that the situation makes a case for increased use of body cameras.

Pressley declined to respond to an open letter from Leary on behalf of the Boston Patrolmen’s Association, urging her to “reconsider” her support. Pressley told reporters she would address the police union official’s comments directly.

In a phone interview with WGBH News Tuesday, Leary defended the record of the Boston Police.

“We don't arrest people frivolously, we arrest people because they're committing crimes, and we don't want our police officers assaulted,” he said. “They're just trying to do their jobs, and people are throwing things at them, calling them terrorists, all kinds of crazy names. ... We're just trying to keep the peace.”

According to Leary, four officers were injured during Saturday’s event.

In a string of videos posted on social media following the protest, BPD officers were seen using what appeared to be pepper spray, putting counter-protesters in choke holds, and pulling counter-protesters down into the street to conduct arrests.

The Boston Police Department did not respond to requests for comment.

WGBH News’ Saraya Wintersmith contributed to this report.