Since Winter '17 (v38.0)

You can get the secureURL using the SiteDetail object

Site mySite = [select Id from Site where Name = 'MySite'];
SiteDetail mySiteDetail = [select SecureURL from SiteDetail where DurableId = :mySite.Id];
System.debug(mySiteDetail.SecureURL);

The mechanism I have found to be most maintainable uses a JavaScript function called by an element's click event, which internally calls an actionFunction to post the form, disables the buttons on the page and then returns false on the commandlink/button. This is used in conjunction with an oncomplete on the actionFunction to re-enable the buttons when the form has been (ajax) posted and returns a result to the page.

Without the rerender attribute the form performs a full postback along with the disabling of the buttons.

Note: You can't disable the button(s) before the form is posted or the data sent to the controller will not include which button/link within the form was clicked and thus which action to execute.

<script src="//ajax.googleapis.com/ajax/libs/jquery/latest/jquery.js"></script>
<script>

    function buttonsEnabled(enabled) {
        // retrieve all of the buttons or links on the page
        // with the css class of btn
        var $buttons = jQuery('.btn');
        if (enabled === false) {
            // add the btnDisabled class to give it the look of being disabled
            // add the disabled attribute to actually disable interactability
            $buttons.toggleClass('btnDisabled', true).attr('disabled', 'disabled');
        } else {
            // remove the css class and the disabled attribute
            $buttons.toggleClass('btnDisabled', false).attr('disabled', null);
        } 
    }

    function doSomeWork() {
        // first, call the action function to post the form
        doSomeWorkActionFunction();

        // second, disable the buttons
        buttonsEnabled(false);

        // third, return false to prevent the click from
        // posting the form a second time
        return false;
    }

</script>

<apex:form>

    <apex:actionFunction name="doSomeWorkActionFunction" 
        action="{!yourControllerMethod}" 
        oncomplete="buttonsEnabled(true);"
        rerender="whateverYouNeedToRerender"></apex:actionFunction>

    <apex:commandLink action="{!yourControllerMethod}" 
        value="Your Text Here" 
        id="theCommandLink" 
        onclick="return doSomeWork();" />

</apex:form>