AS I understand it, their crime was demonstrating in a church. I am not aware of any vandalism or defacement being involved.
I also don’t know if they disrupted a service in progress.
On March 3, 2012, two of the group members, Nadezhda Tolokonnikova and Maria Alyokhina, were arrested and charged with hooliganism. A third member, Yekaterina Samutsevich, was arrested on March 16. Denied bail, they were held in custody until their trial began in late July. On August 17, 2012, the three members were convicted of hooliganism motivated by religious hatred, and each was sentenced to two years imprisonment.
http://rt.com/news/pussy-riot-trial-896/
http://www.bbc.co.uk/news/world-europe-19297373
http://www.theguardian.com/music/2012/aug/17/pussy-riot-sentenced-prison-putin?newsfeed=true
Only after the video of their song criticizing corrupt relationship between Putin and Russian Orthodox Church (Church said before the election that God wants Putin to rule Russia and protesting against the government is blasphemy) became famous in the internet did the police start a manhunt and they were sent to jail for two years. The whole trial was a joke, where for example the poor church guard had to testify how "he was disoriented and traumatized by the events and had nightmares".
Their protest was not a protest against believers. It was against the corruption and inappropriate ties to government in Russian Orthodox Church