Updating UserTerritories via Code

It happens only on Salesforce.com.

Many objects which cannot be updated by Apex are available for updates by web-services. e.g. UserTerritories.
These are still updateable by Webservices API, Ajax Toolkit.

So essentially other systems utilizing SFDC webservices can update it, but not Apex which and is interpreted, executed, and controlled entirely by the Force.com platform.