I was going to add this to the original blue judogi thread, but it would have gotten lost in the traffic.
A LONG time ago, I read in a book that the reason why Kano Sensei came up with a standard uniform for the practice of Kodokan Judo was to remove class distinction. Prior to this, Jujutsu and other martial arts practitioners trained in what was basically their street clothes. As you might expect, how one dressed would reflect upon their station in life. So if you have a wealthy practitioner, you could expect that they would be better dressed to train than say a poor farmer. However, Kano Sensei wanted Kodokan Judo to be practiced by everyone, rich and poor, as a means of physical education and to the betterment of society. By putting everyone in the same white, non-descript uniform, you could not tell a rich Judoka from a poor one. Trainees would be judged on the merit of their training and effort, and not on what social class to which they belonged.
Based on this, I would speculate that the reason a white judogi was used, rather than a variety of colors, is because it was a plain and inexpensive cloth in with to make the dogi. As has been pointed out, the Japanese had raised the dying of cloth in indigo to a real artform. So the availability of a blue dogi (more than just about any other color) was certainly there. However, the dying process was extensive, and the resulting material was quite expensive. So if multiple colors were allowed, and a Judoka of that day wore an indigo judogi, it could be reasonably assumed that this person was wealthy. So you lose the class distinction transparency.