I believe that the real reason is that Webkit needs privileged APIs and unique executable memory regions for the jit. Giving third-party developers that access would make jailbreaking a simpler process.
Anything that makes jailbreaking simpler also makes it easier for the device and data to be compromised.
Apple might have walled garden motives, but the security story is compelling on its own.
One argument I could see being made is that the browser is used more than others and thus warrants tighter control. But even that is weak. People are draining their batteries all day long playing games as it is.