The requirement that the "target" directory be empty is a nuance of DH's "one-click" install. If you install Joomla from the tarball, you will not have this issue.
Bear in mind, that you will need to make sure that you do not overwrite any existing folders when you untar the tarball, or you will break your other applications.
Joomla is easy to install from the tarball using the shell. The process (short version) goes like this:
1) If necessary, create a database to use for Joomla from the Goodies, MySQL options of the webpanel. You may want to use an exisiting MySQL database being used by your blog/forum (during the Joomla install, you can set a "prefix" to be used for the Joomla tables to avoid conflicts with other applications sharing the database) in which case you will not need to create a new database and can skip this step.
2) Place a copy of the Joomla tarball in the base directory of your space using wget or FTP.
3) Untar the tarball
4) Navigate with your browser to your space....... An installation routine will run, and you will need to enter the MySQL hostname, database name, user, password, and a "prefix" for your Joomla tables (Very important if ou are using an existing database!)
5) follow the Joomla installation screens' instructions and you are good to go!