Steeping onion skins in vinegar is a very effective way to color horn, and gives the best antique look I know of. That being said, the problems you mention are indeed a factor to consider. I have found that the coloration of the horn has to be planned from the very start, or the plug swelling issue, and peg swelling issue, will rear their ugly heads. This method is not like the Rit dye method, that is quite fast. The horn has to be steeped in the solution for quite some time, which wreaks havoc with the wooden parts.
Hungry Horse