If the dots were ever connected during the Clinton administration he'd have to go to war - a real war with boots on the ground. In order to avoid this Clinton treated all terrorism as a law enforcement effort as not to have to invade hostile states that aided Al Queda.
I don't think Clinton had the stomach for much more than launching a missle at an aspirin factory. But the reason he instructed Gorelick to erect "the wall" was to stymie investigations into his own criminal foreign campaign money schemes, Chinagate, etc.