Catch 22…you could apply a global query string re-formatting using htaccess, but this will also break CS-Cart's query strings (index.php?dispatch=…). A more specific one would be to strip ?sl=GR from the URL, which you can do so by adding this to your .htaccess, which should be added BEFORE you add any further rules:
RewriteEngine On
RewriteCond %{QUERY_STRING} ^sl=GR$
RewriteRule (.*) $1? [R=permanent]
This would therefore allow you to create simple redirects, such as:
Without then having to worry about ?sl=GR being added to the end of the URL causing a 404 as it has already been stripped out before the redirect is processed.
Also, why not put the language as /en/ in the url? That's much cleaner and you'll be able to geotarget each language as an individual website in google webmaster.