That was an option. I always thought Saddam had a hand in 9-11 in some fashion. There was that training ground where an old jet was, and some indications that Saddam knew 9-11 was coming. Also, it was clear that Saddam was going to work on getting America back at some point, it was only a matter of time. Probably better to eliminate him, but perhaps not, with hindsight.
Since Saddam and Al Qaeda were not natural allies, but had common enemies, I assume that Saddam used his intel networks to give some sort of operational support to AQ, perhaps without knowing they were up to something so big. I can see Saddam wanting to use AQ just enough to hurt and distract the US, short of triggering a massive response.