in the install_cms/diagnostic.php file, the line that checks for safe mode is:
$_SESSION['serverchecklist']['php_notsafemode'] = ini_get('safe_mode') ? false : true;
the ini_get('safe_mode') check must not be returning the correct result. you could edit that to:
$_SESSION['serverchecklist']['php_notsafemode'] = ini_get('safe_mode') ? true : true;
which would force it to true, and bypass the safe mode check.