What I get from the essay is that Ayaz Amir finds the jihad too dangerous a strategy for Pakistan and so he calls for its abandonment; not because innocents get killed or because there is something morally suspect about it. Look at his role models:
There is nothing in Pakistan, not even the 'jihadi' organisations like the Lashkar dedicated to vague causes, to compare with the courage and organisation of Hizbollah. And there is no leader in Pakistan, or indeed across the embattled world of Islam – a religion which we disgrace by our incompetence and cowardice – to match Hasan Nasrullah. So with what weapons in our armoury can we stand up to America and India?It is Pakistan's honor and dignity that is being shredded because its jihadis lack sufficient courage and organization. Islam is disgraced not by the violence of some of its votaries, but by incompetence and cowardice in the pursuit of jihad.
I would like to know if you got the same impression. Maybe my views are colored by many years of reading Ayaz Amir.