controls on free talk and writings and thoughts

On the one hand the government of India wants  to create centers of excellence in higher education sector and I assume that, the purpose of the government is that, as in western universities we want to train our educated youth in  analytical skill, logical reasoning power, free thinking capacity and sharpening of their intellectual capacity  through questioning minds  . What are they supposed to do with all these skills if they can not question any action of the government  or rules which  go against fundamental rights or  human rights or   against the interests of marginalised sections of the population or even against  students interests through non violent, legally permitted and peaceful protests ? If they are intimidated through attack by police ,  arresting  and framing  criminal charges and projecting  them as anti nationals with links with terrorists resulting in disruption of their academic life and future carrier life, a scare is created in their minds which will  turn them into mute spectators of all types   injustice happening around  them . If we convert our youth into such a civil society , it will be a back boneless society . Do we want such an India in future filled with docile population or a dynamic  society acting  as watch dogs of democracy ?