A total of 98 cases of riots have been decided so far in which 1,137 accused were acquitted due to lack of evidence.
Seven people were convicted in a single case related to the murder of two youths, Sachin and Gaurav, in Kawal village in the district.
Nine others against whom charges are to be framed in the case include ex-minister Saeeduzama, his son Salman Saeed, ex-BSP MP Kadir Rana and party's former MLAs Noor Saleem Rana.
The amicus curiae has earlier pointed out that States like Uttar Pradesh, Uttarakhand, Maharashtra and Karnataka have sought to withdraw criminal cases against politicians.
Muzaffarnagar riots: Court allows withdrawal of cases against Suresh Rana, Sangeet Som and 50 others
The accused were booked under various IPC sections for violating prohibitory orders deterring public servants from discharging their duties and wrongful restraint.
Additional District Sessions Judge Nishant Dev acquitted the six accused due to lack of evidence, defence counsel Chandra Vir Singh said.