Comment 56 for bug 460483

At the moment I think the developers of evolution don't want to implement this kind of fix. Seems like they have another idea of how the indicator should be used, but still then their visions are not aligned with the devs of empathy and gwibber. Seems like the folks at Gnome might want to work out a default that all applications should follow regarding the message indicator.
Maybe someone can bring this issue up with one of the evolution devs. I believe there are some pretty strong arguments about the matter in this discussion.

From the Evolution website:
Can I minimize the Evolution window to the system tray?

GNOME includes a notification area to inform the user about some special changes or events. It is not a system tray to minimize applications to. However, you can abuse the notification area to become a system tray by using external software (e.g. http://alltray.trausch.us/).

source: http://live.gnome.org/Evolution/FAQ#Can_I_minimize_the_Evolution_window_to_the_system_tray.3F