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.
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.