Source? The Amnesty International link upthread about his execution does nothing like that, but is criticism of a) the law under which he was sentenced and b) that and how the execution was done (which AI is strongly opposed to and criticizing everywhere)

FWIW, this sounds quite similar to criticism of orgs like them in the west when people also can't understand why they'd defend bad people

Yes he was a terrorist but a repatriated one. India had a policy of bringing youth who have gone the terrorism way, served their sentence et be brought back into the folds of civil political society. Afzal Guru was such a case. Also as mentioned by police high ups who oversaw his case he was a pushover (actual words used "bhondu"). This all turned very convenient for the administration that was under pressure to show progress on the investigation.

The circumstantial evidence found on him related to the parliament attack are of such nature that could easily have been planted by the police (specific example, a scarp of paper with the terrorist handlers phone number found on his person).

Planting of evidence is quite common and rote in India. Judges with a spine discount those. In this case the justice bench didn't -- because the theatre was too important compared to a pushover reformed erstwhile terrorist.