Override Genesis Theme Settings with this handy helper class.

example.php

<?php
/**
 * Using the Genesis Settings Helper Class
 * 
 * @version 1.0.0
 * @author Joshua David Nelson, josh@joshuadnelson.com
 * @license GPLv2.0+
 */
// Reference the helper class by uncommenting below and setting it to the path relative to this file
// require_once '/path/to/genesis-settings-override.php';
add_action( 'init', 'jdn_set_theme_options' );
function jdn_set_theme_options() {
	if( class_exists( 'JDN_Override_Genesis_Settings' ) ) {
		
		$override = new JDN_Override_Genesis_Settings;
		
		// Override Theme Settings - these are all the defaults
		$options = array(
			'update'                    => 1,
			'blog_title'                => 'text', // or 'image'
			'header_right'              => 0,
			'site_layout'               => genesis_get_default_layout(),
			'superfish'                 => 0,
			'nav_extras'                => '',
			'nav_extras_twitter_id'     => '',
			'nav_extras_twitter_text'   => __( 'Follow me on Twitter', 'genesis' ),
			'feed_uri'                  => '',
			'comments_feed_uri'         => '',
			'redirect_feeds'            => 0,
			'comments_pages'            => 0,
			'comments_posts'            => 1,
			'trackbacks_pages'          => 0,
			'trackbacks_posts'          => 1,
			'breadcrumb_home'           => 0,
			'breadcrumb_front_page'     => 0,
			'breadcrumb_posts_page'     => 0,
			'breadcrumb_single'         => 0,
			'breadcrumb_page'           => 0,
			'breadcrumb_archive'        => 0,
			'breadcrumb_404'            => 0,
			'breadcrumb_attachment'     => 0,
			'content_archive'           => 'full', // or 'excerpts'
			'content_archive_thumbnail' => 0,
			'posts_nav'                 => 'older-newer', // or 'numeric'
			'blog_cat'                  => '',
			'blog_cat_exclude'          => '',
			'blog_cat_num'              => 10,
			'header_scripts'            => '',
			'footer_scripts'            => '',
			'image_size'		    => 'full', // or any other registered image size
			'image_alignment'	    => '', // blank, 'alignleft' or 'alignright'
		);
		$override->set_options( $options );
		
		// Remove Theme Settings Metaboxes
		$metaboxes = array( 'breadcrumb', 'feeds', 'header', 'nav', 'breadcrumb', 'comments', 'posts', 'blogpage', 'scripts', 'version' );
		$override->remove_metaboxes( $metaboxes );
	}
}

genesis-settings-override.php

<?php
/**
 * Override theme settings and remove theme settings metaboxes with this helper class
 * 
 * Requires WordPress v2.6.0 and PHP v5.3.0
 * 
 * @version 2.0.0
 * @author Joshua David Nelson, josh@joshuadnelson.com
 * @license GPLv2.0+
 * 
 * Copyirght 2015, Joshua David Nelson
 */

class JDN_Override_Genesis_Settings {
	
	// The array of options to set
	private $options = array();
	
	// The array of metaboxes to remove
	private $metaboxes = array();
	
	// The current option to be set
	private $current_option = '';
	
	// The current metabox to be removed
	private $current_metabox = '';
	
	// Set Genesis Theme Options with array
	public function set_options( $these_options ) {
		
		if( !is_array( $these_options ) )
			return;
		
		$this->options = $these_options;
		
		foreach( $this->options as $option => $value ) {
			$this->current_option = $option;
			add_filter( "genesis_pre_get_option_{$option}", array( $this, $option ), 10, 1 );
			
		}
	}
	
	//Override Theme Option with new value using the magic call method
	public function __call( $func, $params ) {
	    if( in_array( $func, $this->options ) ) {
	        return $this->get_value( $func );
	    } else {
	    	return $params;
	    }
	}
	
	// Get the option's new value 
	private function get_value( $option ) {
		if( array_key_exists( $option, $this->options ) ) {
			return $this->options[ $option ];
		} else {
			return null;
		}
	}
	
	// Remove a group of metaboxes 
	public function remove_metaboxes( $metaboxes ) {
		if( !is_array( $metaboxes ) )
			return;
		
		// Set metaboxes
		$this->metaboxes = $metaboxes;
		
		// Add action
		add_action( 'genesis_theme_settings_metaboxes', array( $this, 'remove_genesis_metaboxes' ) );
	}
	
	// Remove genesis theme settings metaboxes
	public function remove_genesis_metaboxes( $_genesis_theme_settings_pagehook ) {
		foreach( $this->metaboxes as $metabox ) {
			remove_meta_box( "genesis-theme-settings-{$metabox}",     $_genesis_theme_settings_pagehook, 'main' );
		}
	}
}