On which grounds an accussed will be charged of murder by our great 'Supreme Court'?

In Kerala, Onam hangover is not over yet, and it ends on tomorrow only. But since yesterday when the verdict of the infamous Soumya rape and murder is out, festival season is over.

In brief: The incident occurred in 2011 when a 22-year old salesgirl from Ernakulam travelled to her home Shornur in ladies' compartment. It was around 7.30 or 8pm when the whole compartment became empty at Thrissur and a single-handed beggar started troubling her.

Seeing her alone in the compartment he took advantage, and slashed her head multiple times on train's wall. There were many from nearby compartments who saw both jumping (?)/falling out of compartment when train was in a slow pace. He didn't leave her and when she was found around 30 minutes after incident, she was brutally raped and all her possessions including mobile were stolen. She was hit by a stone on her head and she succumbed to injuries three days later. Later the beggar with criminal background was caught red handed, and he was given death sentence in 2011.  

But yesterday, to great shock to everyone, SC dropped murder charge, and "he will be free just after 14 months". His death sentence was taken off on grounds that, there was no eye witness to prove if she jumped or he pushed her out of train (though there were enough evidences that she was attacked in the train and her head was slashed against metal wall, and after all no one in the compartment to rescue the helpless girl). Also, as she died only 3 or 4 days after the incident due to head injuries, he can't be blamed for murder as he did so without any pre-intension. (That means, he jumped out of the train along with her, hit her with a stone on head and committed the crime unintensionally - Right?)

So, my doubt is - On what grounds can one person be accused and punished for a murder. So, as per Indian constitution, if the victim dies, three or four days after the incident though it's not pre-planned, there are loop holes in Indian law to prove him innocent??????? And he will free despite having criminal background, as per Indian laws????