I have many reservations with the author's proposal...and many with the assumptions he builds his argument upon.

Before long, the West may just hold a barrel to al Qaeda's collective forehead. Should it press the trigger?
- How exactly would this happen? Is there any reason to believe that there even is a "collective forehead" to hold a barrel to or is it thousands of foreheads?

Like it or not, keeping a battered al Qaeda intact (if weak) is the world's best hope of funneling Islamist fanatics into one social network -- where they stand the best chance of being spotted, tracked, and contained. The alternative, destroying the terrorist group, would risk fragmenting al Qaeda into thousands of cells, and these will be much harder to follow and impossible to eradicate.
- al Qaeda does not have a monopoly over Islamist fanaticism and they do not operate in one social network - al Qaeda is already generally an umbrella term for thousands of fragmented and chaotic cells that are largely without central leadership or being provided resources from a centralized organization...

The alternative to destroying al Qaeda is to keep it weak -- but alive. The West would need to refrain from attacking all its central parts, choosing to monitor and watch them instead. Al Qaeda would continue to attract Islamist militants into its clustered network, where the fight against terrorism is at least manageable.
- I wouldn't call all the attacks and threats perpetrated by al Qaeda around the world before and after 9/11 a problem that is "at least manageable"

- I would LOVE to hear how "monitoring and watching" al Qaeda could be politically justified by anyone in the law enforcement, military or intelligence community if a major attack occurred under our noses because our intelligence was not as good as the author believes.

Is our intelligence so good that we know which mid level operatives are inept and which are effective? Isn't the way to know that by letting each one of them conduct an operation that would kill people and judge their effectiveness after the fact?

al Qaeda recruits could be shadowed through their training and eventual deployment. New operatives could then be neutralized once they move "downstream" -- away from the network. This timing prevents scattering the higher echelons of al Qaeda, while still eliminating the direct security threat.
This is an incredibly bad idea - lets allow unknown and numerous terrorist recruits become more indoctrinated, receive training, be assigned missions and allocated resources by the most dangerous terrorist leaders on the planet as we watch them and then hope we CAN "neutralize" them once they move "downstream". I hope they don't fall off the radar.

I feel the author is just trying to be thought provoking for the sake of it - not offering any practical solutions whatsoever.