The current Hindu nationalist government didn't resort to violence against the Sikh farmers. Compare that to what they did in Gurgaon after the religious riots, where they practically demolished the homes of the entire Muslim community.

Also, Operation Blue Star was carried out by a secular but hardline government led by a pseudo dictator. Although looking back, it was probably justified considering the Pakistani support for Khali Stan even today. And the Prime Minister lost her life for those actions.

Operation Blue Star was run by Indira Gandhi, the child of an atheist socialist and an atheist Parsi.

It was a hard decision, it was badly executed, but it was not rooted in religious extremism.