TYPO3 Core

think you just configured your server wrong, I have plenty of TYPO3 sites on Debian Servers which works like a charm.

Furthermore I'm a bit unsure if this belongs to tx_realurl

So what could be wrong in the configuration? It is mostly the standard configuration. Additionally, there are the mod_rewrite lines:

RewriteRule ^/cms/(typo3|t3lib|tslib|fileadmin|typo3conf|typo3temp|uploads|showpic\.php|favicon\.ico|index\.php) - [L]
RewriteRule ^/cms/typo3$ typo3/index_re.php [L]
RewriteCond {DOCUMENT_ROOT}{REQUEST_FILENAME} !-f
RewriteCond {DOCUMENT_ROOT}{REQUEST_FILENAME} !-d
RewriteCond {DOCUMENT_ROOT}{REQUEST_FILENAME} !-l
RewriteRule ^/cms/.* /cms/index.php [L]

I tried to review the logic in t3lib_div::getIndpEnv(). The following I got:
TYPO3_SITE_SCRIPT (used in realurl) is build as the difference between TYPO3_REQUEST_URL and TYPO3_SITE_URL
for example
TYPO3_SITE_SCRIPT=path/to/site/ is build from
TYPO3_REQUEST_URL=http://host/cms/path/to/site/ and
TYPO3_SITE_URL=http://host/cms/

TYPO3_SITE_URL itself is build mainly as TYPO3_REQUEST_DIR which is TYPO3_REQUEST_HOST+SCRIPT_NAME
According to http://httpd.apache.org/docs/2.2/mod/mod_rewrite.html , SCRIPT_NAME is the name of the URI before rewriting. As a result, TYPO3_SITE_SCRIPT is always empty, because TYPO3_REQUEST_URL=TYPO3_SITE_URL.
Back to our example, it would be
TYPO3_SITE_URL=http://host/cms/path/to/site/

So i don't know why it works for you, but for me it does not. As I see it, TYPO3_SITE_URL is determined in a wrong way. Maybe it should be something like
$retVal = self::getIndpEnv('TYPO3_REQUEST_HOST').'/'.substr(dirname(self::getIndpEnv('SCRIPT_FILENAME')).'/', strlen($_SERVER['DOCUMENT_ROOT']));
This works for me.

What is different in your environment that this error does not occur?