"The contradictory evidences by police and the NIA in the case raised serious doubts in the whole case," the First Additional District and Sessions Judge of Dewas Rajiv Madhusudan Apte said while acquitting Thakur, Harshad Solanki, Vasudev Parmar, Ramcharan Patel, Anandraj Kataria, Lokesh Sharma, Rajendra Choudhary and Jitendra Sharma.
Joshi, once a close aide of the Sadhvi before they fell out over some dispute, was shot dead in Madhya Pradesh's Dewas on December 29, 2007 in Audyogik Police station area.
Thakur, also an accused in the 2008 Malegaon bomb blast case, is in judicial custody. She was not present in the court when the verdict was pronounced as she is undergoing treatment in Bhopal.
"My clients were absolved due to the contradictory evidences of Industrial Area Police, Dewas, and the NIA, which were not found trustworthy by the court. This has been observed by the court in para 124 of the operating order," defence lawyer Raghuveer Yardi told PTI.
"The court has observed that the analysis of evidence gathered by the police and NIA reveals that in the sensitive and serious cases like murder, both the prosecution agencies carried out investigation with prejudice," he said.
"They (the police and the NIA) didn't conduct investigation seriously and the self-contradictory and weak evidences of the agencies were insufficient to convict the accused and the contradictory pari-materia (a rule of statutory interpretation) makes the prosecution highly suspicious," advocate Yardi said quoting the order.
Initially, the probe had hit a dead-end, but later the arrest of a person in Rajasthan led the district police to Thakur and other accused.
The trial was shifted from the district court to the Special NIA Court in Bhopal a few years ago. However, the matter was shifted back to the district court in September 2014 on the ground it was a murder case and does not come under the ambit of the NIA, which is an anti-terror probe agency.
Public Prosecutor Girish Munji said the state will take a call on challenging the order in the competent court after studying the judgement.
Like Thakur, Solanki, Lokesh Sharma and Choudhary too were not present in court.
While Solanki is lodged in Ajmer jail, Lokesh Sharma and Choudhary are in Panchkula prison in Harayana.
Lokesh Sharma and Choudhary are also accused in the 2007 Samjhauta Express blast case.
Accused Jitendra Sharma, Ramcharan Patel, Kataria and Parmar were present in the court.
Hearing the verdict, Parmar and Kataria broke down.
The supporters of acquitted persons shouted slogans in the court premises after the verdict.