First let's see this image here -
View attachment 153510
This is the Gyanvapi Mosque. The Outer walls is the remnant of the Kashi Vishwanath Temple. It was demolished and converted to a Mosque. This is one of the most important of Hindu religious sites. Not just another temple... so anyway... in case I want to go and worship in this ex-temple, I will be arrested and put behind bars for inciting religious hatred. This is just one example.
Your post is a melting pot of differing ideas, I must tell you that.
You have tried sugar coating many statements as well. So let's see one by one in a rational way.
1. India has been tolerant to foreign thoughts, practices, faiths etc. You have stated that except for Punjab and Bengal the reception of Islam was quite hostile among the Indian populace. I will correct that. The reception of Islam was ENTIRELY hostile and remain so today. And the reception was so even in Punjab as well.
First let me give you the instances of India's tolerance -
o Jews were sheltered
o Parsis were given refuge
o Tibetans were and are given refugee status and even allowed to work as a 'Government'
o Sri Lankans, BDeshis etc etc
Now let me tell you why India's tolerance fails to extend to Islam. It's mostly because of the way Islam was introduced into India. But for small hamlets of Kerala, the first (most important) impression of Islam the people of the Indian subcontinent got carried with it gory experiences of mass murder, wars, torture, repression, defeat, rape and destruction. So what kind of reaction do you expect from the native people?
2. Secondly, you state that mediaval India was engulfed in orthodoxy - namely caste related issues. In this case, you are right. It truly was a dark age. But then this has nothing to do with the topic at hand ie Nehru, or India's allegedly 'Secular philosophy'. Suffice to say that the first baby steps to remove the caste rigidity was undertaken by Indians only - there were plenty of reform movements. Many of them originated in Bengal as well.
3. Your final paragraph is one that emanates fear, fear of the Muslims. The idea goes like this - the non Muslims can be denied of a few rights and no hell will break loose. But if some special privileges are not granted to the Muslims(even if they are not practised in reality), the Muslims will tear the country apart. Who knows, the Hindus and Sikhs may also jump into the fray. So to prevent that, let's suffocate them all, except the Muslims, to make sure religious consciousness remains limited. The fear of the riots, the simple fear of it itself prevents us from making decisions which even we know are right. And the center/the left have
perpetuated this fear even after almost 70 years of independence. That is stay within limits otherwise the Hindus and Muslims will do what they fear comes naturally to them - riots. In reality it is just plain cowardice.