they inherently know the crime they are committing is wrong

If we extrapolate from the other Andamanese tribes' mythology, and commentaries going from the 19th century to the last remaining Great Andamanese elders nowadays, they probably think outsiders -especially light-skinned ones- are undead. And their history can only tell them they're extremely dangerous. So no, from their point of view, they most probably acted in self-defense against something that's not quite human.
These people have been almost completely isolated for the last 50,000+ years.

From a legal standpoint, they're a sovereign tribal nation inside India; that is, India vows to protect them from outside harm (like illnesses or illegal loggers), and to protect outsiders from them (i.e. rescuing shipwreck victims), but that's it. Islanders are only subject to their own laws and customs. They don't even know what India is.
So if the missionary had been spotted alive from one of the helicopters that patrol around the area, the Indian army would have rescued/arrested him; but since he's already dead, India doesn't actually have the right to prosecute the islanders, as they're not exactly subject to their legal system. The only thing they can do is recovering the body if conditions allow to do so without great risk for both soldiers and islanders.