The Mujahid group that was the least Islamist was led by the heir of a religious order and structured as such.
The OP's assertion are fully accurate. The CIA knowingly funded and fomented the rise of Islamic fundamentalism.
It is incorrect the relationship was fully indirect. The CIA directly met with militant Islamic fundamentalist groups, including inviting leaders to the USA, and directly funding them :
https://books.google.com/books?id=b95MAgAAQBAJ&q=cia%2C+bin+...
https://books.google.com/books?id=wcljXYTZVnUC&q=rABBANI,+re...
https://books.google.com/books?id=r3TLByMXsJkC&q=thatcher,+h...
https://books.google.com/books?id=N8Qxf-33dxMC&q=howard+hart...
https://books.google.com/books?id=-R13CgAAQBAJ&q=zalmay%2C+g...
https://www.usnews.com/news/world/articles/2008/07/11/afghan...
http://www.aljazeera.com/indepth/features/2012/01/2012126145...
The evidence is absolutely crushing. The statement of the OP is not misleading at all - it is completely accurate.
And the primary reason the CIA met directly with groups was to cut the ISI out of the picture and give them more direct control over to whom and how aid was provided.
If you read the sources I linked, you will see that the CIA directly met with and financed Haqqani, which was one of the most extreme and who went on to be instrumental in the founding of Al Qaeda by greatly assisting Bin Laden in Afghanistan and allying with him.
That is to say, unequivocally, the CIA directly funded and abetted the rise of Islamist fundamentalism.
My impression was that effectively, their decision at the time was: (a) fund moderate elements who weren't gung-ho about actually risking their forces to kill Soviets vs (b) fund religious extremists who were a more militarily effective option.
And even given that calculus, they still spread the money around (or even skewed it towards moderates), because even at the time they were uncomfortable going all-in on someone who took his orders from God.
The CIA only ever directly financed the more extreme elements that I know of. The more moderate ones, ironically, got all of their funding through Pakistan, though Pakistan gave more to the extremists.
If the CIA gave them more money because they wore more effective, it doesn't change the fact that they directly fomented the rise of Islamic fundamentalism.
That seems incomplete enough to be a misleading statement. Ghost Wars (Steve Coll) is as authoritative and well-sourced treatment as I've found.
It lays out the imperative as "confront the Soviets in Afghanistan." To that end, the State Department and CIA continually bickered over who to best fund and arm in Afghanistan.
Add in the added complexity that most funding was run through the Pakistani ISI, but paid for by the Saudis and Gulf states, all of whom generally had no compunctions and/or outright preference for Islamic fundamentalists (Pakistan due to India, Saudis due to portions of the royal family).
And on top of that, you had a constant realpolitik (arm who will fight, and who our allies will support) vs ideological (arm who believes more in democracy) debate going on. Generally speaking, the Islamists were willing the right, but the moderates tended to find reasons to avoid committing their forces, despite being paid to do exactly that.
So an accurate statement would be "the CIA helped funnel Saudi money to Afghani mujahideen, with Pakistan's ISI steering large portions of that towards Islamist groups, a practice which the US generally knew about but saw no way around."