Magento 2 JavaScript – How to Disable JQMigrate Logging

This depends on the Magento version. For version CE 1.7 the piece of code you wrote is commented out. In 1.6 and lower it's not.
Knowing this, I assume it's safe to comment the code and not worry about future upgrades.

You will need to use spconfig object. Replace your catalog/product/view/type/options/configurable.phtml code with below. I have used the onchange="spConfig.getSelectedIndex()" onchange function.

<?php
$_product = $this->getProduct();
$_attributes = Mage::helper('core')->decorateArray($this->getAllowAttributes());
?>
<?php if ($_product->isSaleable() && count($_attributes)): ?>
    <dl>
        <?php foreach ($_attributes as $_attribute): ?>
            <dt><label class="required"><em>*</em><?php echo $_attribute->getLabel() ?></label></dt>
            <dd<?php if ($_attribute->decoratedIsLast) { ?> class="last"<?php } ?>>
                <div class="input-box">
                    <select name="super_attribute[<?php echo $_attribute->getAttributeId() ?>]" id="attribute<?php echo $_attribute->getAttributeId() ?>" class="required-entry super-attribute-select" onchange="spConfig.getSelectedIndex()">
                        <option><?php echo $this->__('Choose an Option...') ?></option>
                    </select>
                </div>
            </dd>
        <?php endforeach; ?>
    </dl>
    <script type="text/javascript">
var spConfig = new Product.Config(<?php echo $this->getJsonConfig() ?>);


spConfig.getSelectedIndex = function ()
{
    for (var i = this.settings.length - 1; i >= 0; i--)
    {
        if (this.settings[i].selectedIndex == 0)
        {
          alert('yes');  
        }
    }
}