Sirji Power of the state assumes justification. nothing is without justification. The Justification is the Law and Constitution. Even the death penalty has to be Justified. A civilian however does not have that power or right EVEN in self defence - he is still tried and has to defend himself in a court of law and even in self defence he can be sentenced to prison.
Encounter is actually armed police action and are absolutely acceptable - not extra judicial killing. Cops use the cover of encounters to do Extra Judicial Killings is besides the point here.
Keep in mind what i am saying is that The Armed Forces / Police have the power to take life not commit murder.
Justification is not the law that act has to be justified within the ambit of the law.
Secondly, right to life in Article 21 of the constitution within its ambit includes the right to self\private defense which is further enumerated in section 96 of the IPC which reads as "Things done in private defence. —
Nothing is an offence which is done in the exercise of the right of private defence. "
I know of a couple of cases where the person who acted in self defense and killed someone did not even spend one day on jail and in all cases the IO (investigating officer) was an honest man he did proper investigation and filed the closure report stating that it was justified homicide and I know of one instance when a person acted in self defense was jailed for one year because the IO asked for a bribe and the guy did not pay it, but eventually the case was dismissed as the prosecution did not have any evidence to prove the murder charges that were bought against him.
Moreover, there have been several Supreme Court judgements where right to self defense of civilians has been affirmed.