One correction: the Zones impact BOTH the speed of computation AND the laws of physics (whether FTL travel and communication are physically possible). They also make pretty explicit in Fire Upon the Deep that mechanical failure rates of certain complex systems (especially automation) increase rapidly as you approach the Slow Zone. And then within the Slow Zone they increase again as you approach the Unthinking Depths.
It is made explicit -- as you note -- that the Zones of thought are controlled somehow by the Countermeasure (or some Control System it speaks to). It is also clear that this system do not like the Blight and actively opposes it.
One other interpretation that struck me is that the Control System may have put in place the Zones of Thought simply because stars become so dense as one approaches the Galactic Core. Forcing the Transcend to the Galactic edges limits the rate at which any change can spread and allows for civilizations (and the System itself) to respond to threats such as the Blight.