I have not been able to achieve perfect stitch balance on any of my machines using two different color threads. I believe it depends a lot on the specific machine.
In your situation I would make up a test sandwich and try a few different threads before deciding. I would probably go with very fine thread in a light charcoal gray. I would probably try out Invisafil thread for this, or Aurifil 50 wt (which is 2-ply, a good choice if you prefer cotton), or a silk thread if your machine can handle 100 wt thread (extremely fine). In my opinion you want to avoid any regular 50wt 3/ply thread and go with at the very least a 50/2 or 60/2 weight thread. These are threads that will give your quilting definition but will not be highly visible.
Edit: Bottomline in both top and bobbin would be another possibility.
Note: I am assuming you are quilting on a domestic machine. Some of these threads may be too weak for the speed of a longarm.