That would be as a counter intelligence purpose. Here the CIA wanted to befriend alqaeda. But not directly. So they went through an ally intelligence route.
I think that's a stretch, but Al Qaeda was basically eradicated or forced into hiding between 9/11 and the beginning of the Afghan invasion in a desperate attempt to keep the US from attacking. Al Qaeda was in essence a name for bin Ladin's bank account, because he was doing VC funding for training fighters and making audacious attacks against the US and the Saudi royals. That financing source was cut immediately, and Ladin-financed people trapped in Afghanistan had to figure out how to escape a country filled with locals who thought (correctly) that the US was going to come and murder everybody because of what these foreign fighters had been doing.
After that, the US called everything in the Middle East that it wanted to kill "Al Qaeda" and made "The Taliban," i.e. the local government, somehow "Al Qaeda" too, or maybe even worse.
What was "Al Qaeda" and what was "Freedom Fighter" was based on whether we wanted to topple the government or not and unrelated to any qualities or beliefs of the groups. We poured money and weapons into some radical Islamist groups while executing others.
