The CIA probably does fear Bin Laden has access to such technology, or atleast they might use it as an excuse to go in and fuck up some more muslims - hmmm, who has the most oil that we can exploit? Well, they're harbouring Bin Laden and his EMP technology, lets get em!!!
I suppose EMP technology would be good for terrorists to have (in their opinion that is) as they have little in high-tech electronics compared with their enemy. I'm not sure how much good it would do them though really - I suppose they could use it as a defense against missiles (try to disable them before they strike), but as an attack on foreign soil the device would be far too large to transport easily and it's effects wouldn't be as severe and visual as other means of terrorism.
Not sure how it would change foreign policy - I would assume that the US would become more aggressive against suspected terrorists and the nations harbouring them if the threat was 'real'. Militarily, it would depend on the efficacy of the EMP device - worst case scenario it would put the military and terrorist groups on equal ground (everyone would have to use their own eyes and ears) although the military would still possess satellite imagery if required.