Serving an EE site from an Apache Alias location?

We are doing an EE subsite for possibly one of a couple of EE sites under a primary domain which is not an EE site. Our developers have it setup so that some code on the site is outside of the primary htdocs. We are doing deployments via capistrano which changes things as well. Our directory structure looks like this for the main site:

/sites/primarydomain.com/htdocs/

subsites then look like so:

/sites/primarydomain.com/subsites/subsitename/current/htdocs

current is a symlink to /sites/primarydomain.com/subsites/subsitename/releases/releasehash/ which then contains the EE directories

config/ 
stash_templates/ 
system/

as well as our capistrano deploy directory. Our issue of course is that you cannot easily setup an Apache configuration where you insert the EE subsite using:

Alias /subsite /sites/primarydomain.com/subsites/subsitename/current/htdocs/

So that it all appears as www.primarydomain.com/subsite/ There are system_path, APPPATH, BASEPATH, EE_APPPATH, and a few others, none of which appear to be paid attention to seeing as many includes seem to use something like:

include($_SERVER['DOCUMENT_ROOT'] . "../system/file.php");

Is there a guide/blog-post somewhere which might deal with this issue? Or should we create a define to point at the document root of where the code is (were it its own site), and modify all includes like the above code to use the php define instead?