I dont think you can tell any sovergian country to do what we want. And they are not banning common people, just the fundamentalist groups just like you would do with taleban and jamait-e-islami. Also I do not see any reason why Nepal shouldnt be a secular country as long as it remain a democracy and not chinese dominated maoist communist state.
the Hindu fundamentalist should refrain themselves from doing such idiotic acts or we will end up with another headech if Nepal turns into maoist state just like they created muslim kashmir. If the kashmiri pandits had agreed to ladakh's king there wouldnt have been any muslim dominated Kashmir neither today's headech of pakistani militancy.
Listen to what people want and do not try to enforce what you want.