The person refusing to accept an opinion still remains Indian citizen and entitles all Constitutional rights! The Fatwa asking for killing must not be treated as an opinion rather treated as an open provocation to do a murder against cash reward, which is a crime.
Similarly Khap Panchayats issuing dictates must be declared illegal. There can't be parallel Panchayats to constitutionally provided Panchayati Raj system. Further Khap Panchayats some time became the prosecutor, adjudicator and punisher (say hangman)!
In North Western India, Some Khaps not only medieval but also delivers brute punishments to the victims. In most cases, Murder is usual punishment for defying Khap. But in some cases like Bengal Khap verdict and in some other place also, girls were gang-raped because they dared to complaint that certain influential people misbehaved with them! Unfortunately political parties always closed their eyes on such inhuman and criminal social acts because of vote bank politics!
In recent Shankaracharya controversies, first one is, Puri's Shankaracharya refusing to worship Lord Jagannath on Rath because he felt insulted when government didn't allow his associates to board on the Chariot! He perhaps expected there would be uproar among the public and devotees because of his opinion! But none cared! More than ten lakh pilgrims participated in car festival! That means people are aware that Shankaracharya's personal problem is his personal right! For devotees, only Lord Jagannath matters!
In another incident, Dwaraka Shankaracharya opined that Shiridi Sai is not a Hindu God! OK, it's his opinion and may be accepted by his followers! Sai followers disagreed. That disagreement is also their right on their faith! Problem started when Sai followers organized protest marches against Shankaracharya's view and burnt his effigy!
Under provocation Shankaracharya too threatened that Naga Sanyasis would attack temples where Sai is worshiped along with other Hindu Gods. Now there is a confrontation and may escalate more. In my opinion if such things escalate to violent acts, then both Shankaracharya and Sai followers must be booked! Because for the sake of their faith, they can't create disharmony and break the law of land!
The bottom line is faith, religion, rituals, traditions etc are always a private affair of an individual. As long as there is no violation of law of land and breach of fundamental rights of an individual guaranteed by the Constitution! As per the Constitution all are equal share holder of this democracy and all have equal rights too. Thus none can impose or enforce any private thing not endorsed by the law of the land as well as the Constitution.
But who will ensure it? Uma Bharati burnt her finger in the matter of Shankaracharya versus Sai followers! She and BJP is afraid of Hindu votes (in fact both Sai followers and Shankaracharya followers are Hindus). In Puri's Shankaracharya case, BJP raised its sword against BJD government for insulting the seer, forgetting that the seer too insulted Lord Jagannath by declining to perform the ritual!
In Khap cases, no political party ever raised their tones because of fear of loosing votes; forget about traditional political parties, even the new revolution AAP too didn't muster courage to oppose Khap rulings!
Regarding Fatwa, minority vote bank champions never raised their voice, because going against one Mufti/Moulavi/Qazi means loss of thousands of votes. It's another matter that because of such religious encroachment (by all religions) in to polity, an ordinary common-man gets victimise where as the flag bearer of democracy, the so called politicians remain silent against such whimsical orders by religious heads.
Time has now come to separate the polity from religion. Religion has its own space so is the democracy and the Constitution. None should violate the Laksman-Rekha, else there would be chaos! Both religious representatives as well as political representatives must realize this!