DM3's lighting is already ugly, and there are practically no "moody shadows" in there anyway, so a little ambient minlight won't make matters worse.
Here's a commandline I just tried (with AguirRe's light tool):
~/quake/tools/bjptools/bin/light -sunlight3 60 -light 20 -soft -extra4 dm3.bsp
Experiment with the value of -light as you see fit. Sunlight 3 is much the same thing, just applied to outdoor areas and areas close to sky only.
You can add -sunlight 250 if you want a more regular sunlight effect in the outdoor sections. Unfortunately you can't really angle the sun or do anything overly complicated, because there are a ton of point lights floating around to simulate the sun. You'd have to remove those and relight the map a little if you wanted a real improvement, but that'd require use of a map editor.
I never understood why the multiplayer community isn't just switching to Than's remake of DM3.
http://www.quaddicted.com/reviews/dm3rmx.html