Well, back from compositing hell. I think the time spent with the compositor is finally paying off. I also completely redid the asteroids from scratch and got rid of the sun lamp which was nothing but a hindrance. The whole scene is now lighted by a single emitter plane, which generates a lot less noise and allows for better results in shorter times. With the sun lamp I had to use 2000 passess (12 min @720p) and the final render still looked rather noisy. Now with a single emitter plane I can get a very decent render at a mere 500 passes (2 min @720p). Heck, even each single pass runs faster than before.
So here is the present state of my scene:
@DDD: You pointed that I should turn down light sources comming from the right. Well, it turns out I didn’t have any light sources comming from that direction.
What produced the lighting from the right was actually light bouncing off the asteroids on that side of the scene. It probably seems too much lighting from the right because of those asteroids were too glossy. In any case, here is a render of the present scene without the asteroids.
The lighting setup is the same in both renders, but since there are no asteriods to reflect light in the sencond render, the ship looks much darker.
You also asked what I would need Alpha Over for. Well, if you have a look at the ship, you’ll notice that there are actually two emitters there (the white-blue trail material and the white-orange material on top of the engines). I wanted to add a bloom effect to both of them, but tuning the intensity independently for each one. I also wanted to add some blur to the trail. None of these would be possible adding fog-glow to the whole scene.
I managed to do what I wanted by using material index render pass and emitter render pass. I even managed to pull it off using one single render layer, thus saving in render time. 
Finally, here is my updated to-do list:
-Better materials for model.
-Add further detail to the model.
-Texture model.
-Tune DOF effect a little bit (asteroid in the upper right corner looks too clear cut).