How is this a meaningful distinction whatsoever? There are countless apps that allow you to sign up for an "always on" service. Should they be exempt from allowing you to delete your account as well? Or is that privilege reserved for built in bloatware?
iCloud is part of the operating system, and, most importantly, it is not downloaded through the App Store.
These rules are for apps on the App Store.
Edit to add: There may be a reasonable debate to be had over whether there should be some visible component of iCloud that has to be downloaded from the App Store before it can be used on an iDevice—or whether the App Store rules should be, by some means, applied to the entirety of what can/does run on an iDevice. But right now, neither of those are the case, and thus, though some may find the difference between "iOS" and "application running on iOS" frustratingly slim, Apple is not, in this instance, applying its rules inconsistently.