I don't even have a problem with assisting the Mujahedin resist the Soviet Invasion...

As nanne points out, the reality was different from what most Americans believe - that the Soviets invaded and the US then provided military aid to the noble rebels:

Brzezinski: ... But the reality, secretly guarded until now, is completely otherwise Indeed, it was July 3, 1979 that President Carter signed the first directive for secret aid to the opponents of the pro-Soviet regime in Kabul. And that very day, I wrote a note to the president in which I explained to him that in my opinion this aid was going to induce a Soviet military intervention.

Q: Despite this risk, you were an advocate of this covert action. But perhaps you yourself desired this Soviet entry into war and looked to provoke it?

B: It isn't quite that. We didn't push the Russians to intervene, but we knowingly increased the probability that they would.

Q: When the Soviets justified their intervention by asserting that they intended to fight against a secret involvement of the United States in Afghanistan, people didn't believe them. However, there was a basis of truth.

http://globalresearch.ca/articles/BRZ110A.html

Cf.Robert Scheer:

The movie does not mention that the mujahedeen went to war against the Soviet-backed government then in power in Kabul after the government committed the unpardonable crime of allowing female students to attend rural schools. The film casually notes that Gen. Zia, the U.S. ally in this effort to bring "freedom" to Afghanistan, was, like so many of the movie's heroes, a hard case full of contradictions, as exemplified by his having murdered Pakistan's previous ruler, Zulfikar Ali Bhutto.

Bhutto was, of course, the father of Benazir Bhutto, killed last week in Pakistan. What is not noted is that not only Zia but every ruler of Pakistan since him, including Benazir Bhutto, supported increasingly virulent forms of Islamic fanaticism in Afghanistan, ending with the Taliban and the al-Qaida terrorists who attacked America on 9/11, and that all rulers of Pakistan enthusiastically amplified the successful effort initiated by Benazir's now mythically beloved father to build an Islamic nuclear bomb.

... his time, the subject of our nation-building fantasy does have weapons of mass destruction and, thanks to our previous military sales of advanced jets, the means to deliver them. This time the blowback price of our incessant meddling could prove quite high. Even Tom Hanks can't put a pretty face on that one.

http://www.truthdig.com/report/item/20080101_what_good_time_charlie_brought/

As to reason for the film's evasion of the connection to "the 9/11 thing" - from the alternet link you included:

Melissa Roddy, a Los Angeles film-maker with inside information from the Charlie Wilson production team, notes that the film's happy ending came about because Tom Hanks, a co-producer as well as the leading actor, "just can't deal with this 9/11 thing."

http://www.alternet.org/story/73010/?page=2

One bit of accuracy in the film relates to your comment about Charlie's angels:

Crile recounts with relish Wilson's partying. There are many anecdotes of his overseas travels, first-class at taxpayers' expense, accompanied by former beauty queens who seem to pop up at events in conservative Islamic countries wearing skintight jumpsuits.