The main reason that India fares better than Pakistan is that we, in India, have fewer fundamentalist fruit cakes as a percentage of population than Pakistan does. In India the rabid sangh parivar elements are far fewer (definitely more cowardly) than the various Jamaats found in Pakistan. Since their cowardly pack is a bit smaller the harm that they do is lesser.
There are also more robust institutions in our country that will highlight and hound these fundus fearlessly as compared to Pakistan. There are comparitively better judicial systems that rely more on laws of 'Natural law'. Pakistan does have the disadvantage where they believe that what the Umaah does is right even when it can be blatantly wrong whereas in India we are more balanced and fair in our assessments.