It's hard to say, but it could very well be a combination of things. First and foremost, though, the Japanese wouldn't really care how the city name was spelled, because they don't use the Roman alphabet.
I was going to suggest that the writers might've thought they were getting in a small jab by over-Latinizing the name, but then it occurred to me that Italy was also an Axis power. Given that Italian doesn't recognize the letters J, Q, W, X, or Y (except in foreign words), that may have been an era concession, somehow. Maybe.
A web search confirms that this is the common spelling throughout Eastern Europe and a few Western European countries. That makes me think that it was simply the dominant spelling and the "Greek" spelling won out in the following generation. If I had to guess (with no knowledge of Japanese beyond being able to tell you where the cat is in the room--thank you, PBS), I'd suggest that the pronunciation might be a hair closer, and could have become more common to help the occupying forces communicate (tok-yo versus toke-ee-oh).
Of course, I'm talking out of my...let's say "hat," since that's a comparable idiom, and it doesn't really answer your question. It's an interesting topic, though, and I might take another crack at getting an answer overnight.
