Using str_replace on wp-admin

I haven’t tested this code, but I think it will work for you. I just put add_filter after the function and chose preg_replace:

<?php
/**
 * wpse_replace_version_message
 */
function wpse_replace_version_message( $html ) {
  $html = preg_replace( '<span id=\'wp-version-message\'>You are using <span class="b">WordPress 3.4-alpha-19904</span>', '', $html );
  return $html;
  }
add_filter( 'admin_print_scripts-index.php', 'wpse_replace_version_message' );
?>