First, create a file somewhere (for example ~/.devilspie/minimize_evolution.ds with the following:
(Note I do not have Evolution installed, so it's application name might be different, you can find out with running devilspie with a file containing and nothing else)
(is (applicatio_name) "Evolution")
(begin (minimize) )
Then you could do something like
It basically runs devilspie with a rule to minimize evolution in the background, saves its PID to variable xxx, launches evolution, launches empathy minimized, waits 10 seconds (you can make this longer if it takes evolution a long time to start) and then kills devilspies. If you did not kill devilspie, it Evolution would keep minimizing when you would interact with it later. Hope this works, I have tested this only partially.
devilspie ~/.devilspie/minimize_evolution.ds & xxx=$!; evolution & empathy --start-hiden & sleep 10; kill $xxx