This post struck the nail right on the head!!! Copper or brass can be quenched or allowed to air cool and the end result is the same. When it comes to brass cartridge cases it matters how long they are heated and also to what temperature. If too long or too hot they will become dead soft and the neck wont have the required tension {memory} to properly hold the bullet.
As to the discoloration, I would suggest you try a small piece in some acidic water and see. White vinegar will lower it enough if you test it with a ph kit. You don't need it too low either. I haven't annealed a lot of bare pure copper, I mostly did steel prior to heat treating, but what I have seen is that it will discolor some. As suggested, what I saw turned bright pink, definitely not darker.
Edit: you might want to make sure the copper is perfectly clean before you heat it up too. "Lemi-shine" will clean it up nice and might not work too bad as you pickle quench additive. Cheap enough to try.