You are missing the main point of the article.
So the Pakistani government 'allows' it to at least appear in control.
They're supposedly developing longer-range capability capable of hitting some of Europe[1], but right now they might be able to hit some US military bases in the middle-east[2].
I'm not saying Pakistan isn't corrupt, but pretending that they could simply switch from their current US-friendly policy to a strategy that's openly adversarial to US-interests seems to blatantly ignore the realpolitik of the situation.