In a democracy judiciary, legislature and executive are independent of each other. Judiciary has the responsibility to ensure constitutional provisions are not violated.
Criticism of judiciary about coal scam is justified as the investigation was asked for by it. But judiciary wanting an affidavit by July 10 on making agency autonomous (reported in times of India of may 9, 2013) amounts to taking over the function of legislature.
Incase CBI has to be autonomous, who will appoint the functionaries? Should the functionaries be form the IPS, which is part of the executive? Or, as in case of election commission (which is autonomous) the president of India appoint them. IPS and state police force should have nothing to do with CBI. Is this arrangement possible? In my view judiciary should give comprehensive guidelines for formation of CBI as an autonomous body without infringing upon the independence of legislature and executive.