What a nonsensical article and what a nonsensical thread.
Apparently there is supposed to be a big deal made about the fact that some people in Pakistan might explore alternate avenues of spirituality from those taught them by their parents? Yousuf Youhanna converted to Islam and became Mohammed Yousuf - I paid no attention, and it really shouldn't have been given attention, because conversions by small sections of society are pretty routine everywhere in the world.
Now, I do see a degree of intolerance and disrespect for those Pakistanis who become atheists. Atheism is in a way a belief system just as is Islam, Christianity or Hinduism, and some people are forgetting that Islam commands us to respect the faith of others, not ridicule them or insult them over it. Pakistani atheists are just as much Pakistani as Pakistani Muslims, Sikhs, Christians or Hindus.
And all that said, I understand that the idea behind the article (which was rather erroneously, but unsurprisingly given that we are talking about the Indian media reporting on Pakistan, titled "Many Pakistani Youth giving up Islam" last night) is to make the implicit argument that somehow Pakistan's 'identity' is being questioned and all the other nonsense and subsequent conclusions Indian commentators often come up with, but the reality from polling data over the last few years has indicated the opposite - the Pakistani middle class and Pakistani youth are becoming more religiously conservative.
As for the role of Islam in Pakistan being diluted, perhaps after 2 or 3 hundred years. Remember that even the US, with a constitution that argues 'separation of Church and State' still has a very strong religious minority that is able to retain significant influence over policy, despite having over two hundred years of representative government and constitutional rule to evolve over. Pakistan does not have the starting point of such a constitution, so Islam is likely going to play a role in the State for a very, very long time.