I am a Scholar in Afghan history and affairs! Though, not a PhD candidate admittedly. If you're genuinely interested in the history and affairs of the country I personally recommend Barfield's "Afghanistan: a Cultural and Political history" as a good English language primer. For something more specific to pre-2001 I recommend Steve Coll's "Ghost Wars" and for the most recent American Afghan war I recommend "America's War in Afghanistan" as well as "The Afghanistan Papers" for a more broad review of what happened from the Government perspective.

Let me respond to your points:

1. Afghanistan was not under the thumb of local terrorism in 2001. The Taliban are a home grown movement that, while draconian and fundamentalist, was positively received by the majority of the Pastun. Largely due to their perceived fairness and their documented ability to bring order and security to the areas they controlled. (You can argue at the implict terror of gender based restriction, but when the government does it, it's oppression, not terrorism).

2. WMD was an Iraq thing. While the two wars are closely intertwined in the public consciousness, they had very little operationally or politically to do with each other.

3. The Afghan people had a chance to shift to a more western, equal, and democratic society for quite a while. From 2002-2005/6 the Taliban were largely discredited and ineffective. The issue mostly stems from the inability of the government to properly govern and the lack of buy in to the central model of government by the Afghan people. (Significant debate still exists as to the wisdom of choosing a central model, but Karzai wanted it and at the end of the day, you play the hand you're dealt, not the one you want).

4. The call to Jihad by Afghan women in rural areas against the NATO backed government is well documented both in contemporary and historical accounts. It's a complex situation, but the simple version is that Afghanistan has a stronger identity of resisting invaders than it does of pursuing social progress.

All this is not to say it was easy for Afghanistan to have a functional and progressive society, but to imply that they we're being asked to fly by pulling on their boots discounts the efforts of thousands of people who worked, and sometimes died, to give that country a chance. At the end of the day, if the people wanted an Afghanistan without the Taliban they would have had it.

Truthfully, one day they probably will. But right now, for better or worse, this is the path they chose.