For seven months, the world got to know Pussy Riot as three women defiantly smirking inside a glass cage as they issued a rare challenge to Vladimir Putin and the justice system that serves him. On Wednesday, the trio was separated when a Moscow court set free Yekaterina Samutsevich, the oldest and quietest of the Pussy Riot three, while ordering her two bandmates to serve the rest of their two-year sentences in a Russian prison colony.

The two women who remain in jail, Maria Alyokhina and Nadezhda Tolokonnikova, smiled through light tears after hugging Samutsevich goodbye. They then placed their hands through an opening in the court's glass cage, waiting for guards to cuff their wrists and lead them away.

The release of Samutsevich prompted much speculation in a country enamoured of conspiracy theories. Her fate overshadowed the fact that two women, both mothers to young children, will not be free until March 2014.

A smiling Samutsevich was swarmed by reporters and supporters as she walked out of the court into an autumnal Moscow drizzle. They applauded and shouted "congratulations". One man chanted "glory to Pussy Riot" like a mantra.

It was a bittersweet release. "I am happy, of course, but I am upset about the girls," Samutsevich said, before being whisked away from the media frenzy.

The case against Pussy Riot, a feminist punk collective formed to challenge the government of Vladimir Putin, has laid bare the crackdown under way as Russia's powerful leader seeks to overcome growing opposition to his rule.

Arrested for singing an anti-Putin "punk prayer" inside a Moscow cathedral that caters to the governing elite, the three members of Pussy Riot maintain they were carrying out a political protest. The prosecution argued that the goal of their February performance was to offend Russian Orthodox believers.

As with statements made during their trial in mid-August, the women used their appearance in court as a political platform. Posted on blogs and circulated via opposition online media, their words have been keenly read by Putin's opponents.

Tolokonnikova, over loud objections from the judge, warned that Putin was leading the country to civil war.

"I want to warn that everything that is happening in Putin's third term is leading to the end of stability," she said. "In two years there will be civil war, because Putin is doing everything to ensure that." The judge did not let her finish.

"We are sitting in jail for our political beliefs," Alyokhina told the court. "And these beliefs won't let me be quiet: if this verdict remains and we go to a prison colony for two years, we still won't be quiet. If we are in Mordovia or Siberia, we still won't be quiet, no matter how uncomfortable that is for you."

"I have lost all hope in the court," Alyokhina added. "I want again, and probably for the last time as I won't have any more chances, to talk about our motives."

"I call on all believers to listen to us, because, dear believers, we didn't want to offend you," she said, staring down a video camera placed in the jury box recording the proceedings. "We went into the cathedral to issue a protest against the fusion of the spiritual and political elite of our country."

In an interview aired last weekend, Putin came out in support of the women's arrest and sentencing, and showed disgust at what he called their "indecent" name. Alyokhina responded by quoting the president and his spokesman: "That is no more indecent than your Vladimir Vladimirovich [Putin]'s statements about 'wasting our enemies in the shithouse' or 'smearing the livers of protesters on the pavement'." Supporters outside the courtroom cheered at her statement.

Pussy Riot's supporters had long speculated that the Moscow city court would find a way to soften the verdict to dampen the outcry over the case. Although supported by most Russians, who embraced the Orthodox faith in the wake of the Soviet collapse and are served mainly by state-run media, the verdict and sentencing led to an outcry with which Putin had rarely before been targeted.

Samutsevich fired her lawyers earlier this month and hired a new attorney to represent her at the appeal hearing. Until then, the women had been represented by the same legal team – Mark Feygin, Nikolai Polozov and Violetta Volkova. Samutsevich's new lawyer, Irina Khrunova, argued that her client should be treated differently to her two cohorts, since she was ejected from the cathedral shortly after entering and so didn't take part in the "offensive" performance. The court agreed.

"There is no split inside the group Pussy Riot," Samutsevich told the court.

"Of course we are happy Yekaterina Samutsevich has been freed," Polozov said. "It's great that one girl won freedom. We will continue to fight for Nadya and Masha," he said, using the diminutive forms of their names.

At 30, Samutsevich is the oldest of the three women. Alyokhina, 24, and Tolokonnikova, 22, both have young children.

The two women are expected to be sent to separate prison colonies within 10 days of their receipt of the judge's written decision. Polozov said he expected the women would appeal to the European court of human rights in Strasbourg.

In a country that thrives on conspiracy theories, speculation abounded. Some said Samutsevich had made a deal with the authorities, others that she had broken under prison pressure.

The trial was marked by procedural violations and absurdities – the judge, Marina Syrova, allowed no defence witnesses to be called, while the prosecution declined to question the three women on trial. Pussy Riot's lawyers likened the case to a Stalin-era show trial. Despite the theories, one view remained: that the trial had not suddenly gone straight.

"The Pussy Riot case is political," wrote Tikhon Dzyadko, a prominent journalist. "There is no independent court system in Russia, especially in such cases. It doesn't matter which lawyer the defendants had." Pussy Riot's supporters have accused Putin of curating the case against the trio.

As Feygin, Polozov and Volkova left court, Samutsevich's father, Stanislav, pushed through the throng to say he hoped they understood her decision to push for her own freedom. He was apologetic. Volkova took him by the arm and said: "Stop it. Congratulations."

He said he felt "huge happiness" upon his daughter's release. "I want her to rest now, normally, at home with her family," said the 73-year-old, who attended every court session. He said his daughter would continue to fight for her friends' release.