I’d assume there wasn’t a lot of incentive to do so, at least not right away. Getting rid of this stuff (especially if it has degraded and leaked) is a dangerous and expensive undertaking. With the new government in place, and Bush probably not expecting Obama to pull out all the troops, there was no urgency to pay attention to a decommissioned chemical plant from the 90s, much less spend American money to clean it up.
The article says it has potentially usable chemical. It must have been far more usable 12 years ago.