Your ignorance is really profound.
Even with a certificate of terrorism, an unarmed man, or woman or child, in police custody or otherwise apprehended or arrested, cannot be killed except by judicial sentence. The Gujarat police are not entitled to kill people on suspicion; there is a judicial procedure to establish guilt, and a procedure to sentence the guilty. Those processes are not with the police.
The IB gave information about suspects, they had no proof then. Such information about suspicious behaviour is not sufficient for anything except arrest and detention. For anything more, the police have to ask a judge. THEY HAVE NO RIGHTS OF THEIR OWN, TO FIND ANYONE GUILTY, TO PASS SENTENCE, OR TO EXECUTE SENTENCE. That is the difference between a democracy and a dictatorship. That is the difference between us and Pakistan under military rule, that we laugh at so much, or between us and China. If you do not believe in the rule of law, amend the constitution. Until you do that, the law stands.
Your point about the IB and the CBI is stupid. Really stupid.
The IB is the intelligence bureau. Its members do not carry arms, they are not concerned with local happenings, crime and punishment, they are responsible for gathering information. They do not file cases, they do not prosecute, they do not furnish evidence. I can give you the e-mail of former IB Directors, and you can ask them directly. When the IB gets information, they have to inform the police whose jurisdiction the suspected trouble comes under. In this case, it was the Gujarat police, nobody else.
It was for the Gujarat police to track the suspects, to establish suspicious behaviour, to seek a warrant, to arrest them, to produce them before a judge for preventive detection, OR to file charges, a charge sheet, and prosecute them through the public prosecutor, supplying the evidence for the prosecution.
The CBI is the Criminal Bureau of Investigation, the equivalent of the FBI, just as the IB is the domestic (not the international) version of the CIA, and looks into crime. It does not look into intelligence, only crime. It has its counterpart in every state, sometimes in cities, as the CID, the Criminal Investigation Department. It can be asked to look at a case only by the permission of the State Government, OR by direct order of a court. The central government can do little by itself unless it is asked to intervene. So the fairy stories about ManMohan Singh or Sonia Gandhi are just that, fairy stories. There are ways for the central government to influence its investigations, but the Supreme Court is making sure that the government gets off its back.
Please understand that a suspicious judiciary called in the CBI, not a political government.