Agreed, but even the founder of Ahmaddiya sect Mirza Ghulam Ahmed believed that Quran was unaltered word of Allah and stated that perversion in the text of the holy Quran was beyond the range of possibility. Ahmadis believe in exactly the same Quran as other Muslims. Just because they interpret one verse differently (and that verse has been interpreted by some medieval scholars in exactly the same way as Ahmadis do, meaning that this specific contentious interpretation hasn't been invented by Ahmadis) doesn't mean that they have nothing to do with Islam. At max you can call them a misguided/heretic sect of Muslims.
But that is besides the point. In a Republic, minorities have certain inalienable rights but when The State starts infringing on the (basic) right to self-identification/personal religious identity of the minority (based upon the will of the majority) it goes against the very essence of Republic .. We have to stop our descent down the slippery slope. If tomorrow the majority of Sunnis declare that Shia are Non Muslims, will the State declare them Non Muslim too ? ...
Any credible source to back up your claim ? And even if the Court had ordered demolition (which it hadn't of course) why use Mullahs and religious fanatics instead of State Machinery ??