Here is a workaround for this problem...
Step 1
Install xdotool...
$ sudo apt-get install xdotool
Step 2
To start empathy in hidden mode just for yourself...
$ mkdir -p ~/.config/autostart
$ cp /usr/share/applications/empathy.desktop ~/.config/autostart
$ gedit ~/.config/autostart/empathy.desktop
...OR....
To start empathy in hidden mode for all users...
$ cp /usr/share/applications/empathy.desktop /etc/xdg/autostart
$ sudo gedit /etc/xdg/autostart/empathy.desktop
Step 3
In section [Desktop Entry]
Replace...
Exec=empathy
With...
Exec=sh -c 'empathy & xdotool search --sync --onlyvisible --class "empathy" windowmove 25 25 windowunmap'
Finally, save your changes; log out and log back in. You will see the Empathy window "flash" for split-second and then it will disappear. Empathy will continue to run in the background, and you will be able to open the Empathy contacts window (from the unity indicator) whenever you want.
Note: If you don't like the command line, install xdotool
using the Software Center. Then use the Startup Applications GUI from the Dash to to create a new launcher called "Empathy," and enter the following as the command: sh -c 'empathy & xdotool search --sync --onlyvisible --class "empathy" windowmove 25 25 windowunmap'
.