Now that a case has been brought to the HC by an interested party, the legality of the Commission is for the court to decide. I would only draw attention to the fact that unless such an interested party raised the issue in court, the court was powerless to decide anything in respect of it. Similarly all criminal cases are brought before the courts for judgement and sentencing in the interest of the nation by the government prosecutors throughout the civilised world, and the government has an inherent right to 'plea bargain' with the 'accused' to get voluntary disclosures and admission to reduce the work load of the police and courts. And the timing and modus operandi of such 'plea bargaining' or any formal charges are entirely up to the government prosecutors ( i.e. the Ministry of Law).
So it is neither true, nor a constitutional obligation that all the criminals and their whole gamut of criminal activities must be dealt with by the courts. However, once the court is involved it has the supreme power to decide an issue ( subject to appeals in higher courts).
If the Truth Commission set up by the government is a bona fide institution having the mechanism (however temporary or rough and ready) to reduce the workload of police investigation and court time, it should be accepted as such without objection, unless someone can litigate to prove to a court an ulterior intention. Mere innuendos or expressions of dissatisfaction in this respect are irrelevant.
Many disputes can be settled outside the courts quite quickly and effectively and every such opportunity must be exploited. Shariah laws also allow such settlement between the aggrieved parties.