As of v.2.0-RC1, Genesis Framework child themes search for a favicon in the child theme images folder and fall back to the Genesis favicon if none is present. I’m working on a theme that calls a multi-resolution favicon from a CDN, so adding the favicon to the child theme doesn’t make sense, and filtering genesis_pre_load_favicon has unnecessary PHP overhead. The solution (in functions.php):

include_once( get_template_directory() . '/lib/init.php' );
remove_action( 'genesis_meta', 'genesis_load_favicon' );
remove_action( 'wp_head', 'genesis_load_favicon' );

You can then add your custom link in header.php:

<link rel="shortcut icon" href="//example.com/favicon.ico" sizes="16x16 32x32 64x64" type="image/x-icon">