Oh wait - I forget the article was written in the UK. They speak English there.
The distinction you make is correct and is important and you're right some Freepers carelessly miss it. However, it is the Times that wishes to blur the distinction -- in English.
Start with the headline:
Damn misleading in my book...
The article alleges that a local government is sheilding al-Qaeda. That's a hell of an accusation and it needs to be backed up with something besides anonymous sources and a vague reference to some arm of a regional government somewhere along a 1500 mile border.
I agree. The title was very misleading. Regional figures being pro-Al Qaeda in Pakistan is not suprising.