> Why would the weapons need to get out?
Non-proliferation, for one. If Turkey goes hardline Islamic and it would get its hands on those weapons that would make it yet another hard to predict factor in Middle-East politics.
> Why wouldn't the weapons be equipped with a self-destruct, or self-disablement mechanism?
Anything that can be added can be removed and likely such mechanisms would not work (for obvious reasons) by remote control.
> Why wouldn't the US destroy the facility if there was a risk of the weapons being used?
Because they were too busy saving their asses? Because raining bombs on Turkey would probably not be a better solution than getting those weapons out while it was still possible?