The suspects, Ghouse Mohammad and Riaz Akhtari, who are accused of killing Kanhaiya Lal on Tuesday, arrived in court in a police van with their faces covered.
Following the posting of a video by two Muslims taking credit for the murder of a man in Udaipur, the police in Rajasthan also outlawed public gatherings out of fear of bloodshed.
Raj Thackeray had previously organised a rebellion inside the Sena and established his own party, the Maharashtra Navnirman Sena (MNS).