-The US invasion of Afghanistan has cost Pakistan dearly. I think the implications of such an attack were not lost on the Pakistani establishment. Nevertheless, Pakistan decided to play along and even allowed for NATO supply lines to pass through its territory unabated. Thus, implying that Pakistan had little choice but to do so. Therefore, Pakistan cannot starve coalition troops in Afghanistan. It just isn't possible.
The environment immediately post 911 is completely different from the environment today.
What characterized the thinking immediately post 911 was, to put it simply, that military force could be used to accomplish complex goals. Afghanistan and then Iraq invaded - what has been learned in the aftermath of that is pretty clear.
Pakistan refusing to cooperate in the immediate aftermath of 911 would have possibly invited military retaliation and perhaps even invasion. But today it is pretty clear that any attempt to do destabilize Pakistan, through a military invasion, sanctions etc. would only destabilize the regional situation further.
Think about it - why do NATO supplies even have to pass through Pakistan? Ostensibly to support the mission in Afghanistan, correct?
And what is the mission in Afghanistan? Stability? Lasting peace? End to insurgency?
If Pakistan refuses to cooperate with the NATO mission in Afghanistan, what exactly can NATO do that will not further destabilize that mission?
-Maybe denying the transit route isn't isolating Afghanistan, but the decision makes no economic sense. It was probably a political move to save face, given Pakistan's current predicament any government that cooperates with India would be setting itself up for disaster.
Also, AFAIK, the gas pipelines are economically viable only if India is in the loop.
There have been very real concerns and costs historically from smuggling related to transit trade to Afghanistan, so the reluctance to grant transit trade to India is not entirely due of political reasons.
I am also unaware of any of the original pipeline deals (TAP for example) having connections to India, though that would not be something Pakistan would oppose. The pipeline deals know proposed initially were for Pakistani consumption and export out of Gwadar. There has been talk of a TAP(I) pipeline, but given India's reluctance to join the far more feasible and advanced (in terms of planning and negotiations) IPI pipeline, arguments of export to India carry little weight. Going by India's past behavior, its not happening any time soon.
Then there is also the question of safe passage through Pakistan and the possibility of economic blackmail over disputed territories.
India seems to have worked its way around Pakistan through Iran for now, but these ongoing disputes are helping no one. Both countries could have adopted a pragmatic approach instead of holding our economic interests hostage over Kashmir. Economic cooperation would give us a stake in each others development, reduce mutual distrust hence minimizing interference from outside powers and give us a real chance of reconciling our differences, but it seems we are more comfortable calling an outsider a brother.
Here you seem to be arguing against Pakistan being used for transit trade with Afghanistan, so I am not sure what your point is since my impression was that you started off arguing in favor of such trade.
In any case, India is obviously welcome to go through Iran. India is not Afghanistan's only trading partner, and Afghanistan and especially the Pakhtun transporters and truckers have beaten a path for trade with the rest of the world through Pakistan for centuries. So long as those shipping and transportation routes remain viable, trade with India or not, the Afghans will continue to use Pakistan for trade IMO.
Just because your my neighbor doesn't mean I leave my door wide open. I'll invite you for tea or dinner, but I'll still leave my door locked. Comprende? 
We need to work together peacefully to negotiate our common welfare. 
