People are complaining about Sanskrit prayers in Kendriya Vidalaya as they are perceived Hindu. It must be noted that Supreme Court has held that Christian schools that take money from taxpayers can hold Christian prayers and also dictate what religious symbols students can and can not wear. Similar freedom is not available to even unaided Hindu schools.
Kendriya Vidyalaya issue now is nothing but an attempt to get foot in the door to kick out anything remotely related to Hindu practices and symbols from ALL schools. After the low hanging fruit of KV is picked the same people will claim what is good for KV should be good for all other schools with usual exception of minority schools.