As much as I hate it, I think in the case of India, preventing religious conflicts is best compared to defending free speech. The amount of police force needed to protect people who in the name of free speech offend religious sentiments and the community that gets affected because of the speech would be prohibitive. Plus, Indians are in general too sensitive about religion in general though that is slowly fading away. We need more success stories of satellite launches and corruption free bureaucracy to start believing in science, democracy, judiciary more than religion. Even now, there are different family laws based on what religion a person is hailing from. This is done so people can still apply their religious morality when it comes to family matters. For many western folks, this can be confusing. I for one have long wanted a uniform civil code in India. When I was raised, I was not told about the indian judicial system and what it means to break country's laws. I was taught about not breaking the hindu code of law. So religion is part of pretty much everyone's upbringing. I know very few strong atheist Indians. (I am transforming from being a theist to an agnostic.) With religion and God, there seems to be a constant hope. With other things, especially in India, people do not have that hope. As far as the modi example goes, supreme court of India did not find Modi guilty. So as per the country's laws, he is allowed to contest elections. He did so and won. People voted for him because he gave them a hope of development. He has been elected chief minister thrice in the state of Gujarat even winning elections after the riots. There is also a number's game here. 80% of Indians are Hindus and only 15% are muslims. The media coverage often cited the burning of Hindu pilgrims in train as the starting point of the riots which probably swayed the voters. What happened in Gujarat is completely wrong but I'd say it happened because some religious fanatics decided to throw propaganda speeches (in the name of exercising free speech) worsening the problem.
I do believe however there is in general liberty to free speech as long as it doesn't involve religious flame wars or speeches filled with national hate (You may want to read up on arrests of pro-LTTE speakers) . The isolated examples quoted in the original article can be argued case by case and as far as I know convictions have not been obtained. So the law is taking it's course. The very act of arresting them is violating civil liberties but there is no strong organization like the ACLU in India (there is PUCL but it's pretty dormant) to help citizens. And common people do not want to spend the money on lawyers and courts. So police force will continue to abuse their powers because no one keeps them in check. I've personally faced police excesses and it was more of a taboo to explain it to your family that you were picked up for questioning. In India, the very act of you being questioned by police is seen as a character issue.
Long story short, when I see first world struggling with civil liberties (I live in USA now), I do not expect India to do better. It is also unfair to compare a much younger democracy with an older democracy that still hasn't figured out civil liberties in digital age completely. I also do not expect India to lead the world in terms of civil liberties in next 20 years (either digital or regular). I do hope the remaining humanity in Indians don't vanish. Otherwise, we'd implode.