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In a wiki family, when these settings are used:

switch ($_SERVER["SERVER_NAME"])
{
	case "fa.localhost":
		$wgLanguageCode = "fa";
		break;
	case "en.localhost":
		$wgDBname           = "enwiki";
		break;
}

$wgLocalDatabases = array( 'enwiki','fawiki' );
$wgConf->wikis = $wgLocalDatabases;
$wgConf->suffixex = array( 'wiki' );
$wgConf->localVHosts = array( 'localhost' );
list( $site, $lang ) = $wgConf->siteFromDB( $wgDBname );
$params = array( 'site' => $site, 'lang' => $lang, 'wiki' => $wgDBname );
$wgConf->settings = array(
	'wgScriptPath' => array( 'default' => '/w' ),
	'wgArticlPath' => array( 'default' => '/wiki/$1' ),
	'wgSitename' => array( 'enwiki' => 'English Wiki', 'fawiki' => 'ویکی فارسی' ),
	'wgLanguageCode' => array( '$lang' ),
	'wgLocalInterwiki' => array( '$lang' ),
	'wgSecretKey' => array(
		'enwiki' => "ce352ddd112c5d9665cf7264f2a6a36b91aebc2242fd2f4ffcbb5a4cd0601590",
		'fawiki' => "5985cc63dbb366e3837cde1868e2f2cfdd6ea0b77bf95510686bc1f1822e4e40",
	),
);

Both the Persian and the English wikis are rendered left-to-right. However, when $wgLanguageCode is set in the top section:

switch ($_SERVER["SERVER_NAME"])
{
	case "fa.localhost":
		$wgDBname           = "fawiki";
		$wgLanguageCode = "fa";
		break;
	case "en.localhost":
		$wgDBname           = "enwiki";
		$wgLanguageCode = "en";
		break;
}

the Persian wiki is correctly rendered RTL.