Start with tray icon only.
In rhythmbox, if you click the tray icon to send it to the tray and then close it, the next time you open it, it will start in the tray.
Gajim should act the same way. I do not want it in my face every time I log in but I do want it to start up in the background.
At the very least, there should be a pref option of "start in tray only" or a command line switch "gajim --tray-only" or similar.
Although mimicking the way that rhythmbox does it would be ideal, since gajim is a gnome application and consistency is a good thing, I would settle with either of these solutions.