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From the admin section with all the modules you cannot disable a module. From there you can only disable the output of some module. This means that the code is still executed but no output is generated.
Indeed, the way to disable a module is to change the tag <active> to false in the module declaration xml (app/etc/modules/Namespace_Module.xml) and clear the cache.
I don't think you can disable a module from code since the modules are loaded very early in the application (Mage_Core_Model_Config::_loadDeclaredModules()).
When building custom modules I also like to be able to disable them with 'one click'. Here is how I usually do it:

• add in the system.xml an 'enabled' field.

  Module is enabled select adminhtml/system_config_source_yesno 1 1 1 1

• create a method in the helper to check this flag

  public function getIsEnabled(){ return Mage::getStoreConfigFlag('section/group/enabled'); //replace section & group with appropriate values. }

Now in every piece of code that is overriding something in the core or is supposed to output something, I use this helper method.
Let's say you are overriding a method called getSomething() in a class. This is how your method should look like:

function getSomething($params){
    if (!Mage::helper('module_name')->getIsEnabled()){ //if my module is not enabled
        return parent::getSomething($params);
    }
    //your logic here.
}

Every .phtml in your module should look like this:

<?php if (Mage::helper('module_name')->getIsEnabled()) : //if my module is enabled?>
    <div>Block output here</div>
<?php endif; ?>

If all your template and overwritten methods look like this, you should be able to disable (simulate disable) from the configuration panel.