I don't see any reason the Rokugan type couldn't be done as ki. The whole idea of four elements with void in the middle is still a mystical concept. In a traditional D&D world, command over the elements might be categorized as a kind of a divine or acane magic but there is no reason it has to be. The PHBII gives monks the chance to throw fireballs with their ki. You could certainly say, "Well, gosh, water elemental control, that makes me think of Fey, so Shugenja should be the Fey power source." But I think there is a confusion there about power sources and power mediums. Monks don't have the "punching and kicking" power source, Fighters don't have the "I like swords" power source, Wizards don't have the "fireball" power source. Rokugan style shugenja could not be martial because they are obviously supernatural, but they could be anything else. Ki is, ultimately, a supernatural power, and manipulation of the four elements sound as valid as anything else you might do with ki. In 3.5, ki already turns people invisible or astral, helps them teleport, heals wounds, throws fireballs, and leads to immortality.
To "4e" the shugenja, I would keep the elemental focus, divorce some of their powers from 3e concepts and focus on powers that make sense thematically, and offer the shortsword and naginata as good weapon choices.
I really don't see your logic here at all. Seriously, I don't. That first paragraph makes me more confused than anything else. It almost seems like you are deliberately trying to confuse the boundaries of "power source" so that anything will fit under any power source, but I don't really think that is what you are intending... Might as well argue against what few bits of data I can pull out...
I don't see "elemental" as having anything to do with the concept of ki at all. Elemental powers that directly refer to a structured system of four or five elements will almost
certainly belong to the Elemental Power Source, since that is all that one has. Certainly, Ki may have a few Fire, Cold, Lightning, Thunder, Radiant, or Necrotic powers, just like Arcane or Divine, but just like those other power sources I don't think it will build such powers under the assumptions of a structured system of elements.
Also, certainly some kinds of "mysticism" are a part of the Ki Power Source, but that does not mean the Ki Power Source will or should be some kind of catch-all for everything mystical. Just like Divine is built around religion and channelling the power of the gods, and Primal is built around totems, spirits, and transformation, Ki will be built around a specific subset of the wider concept of mysticism. As people at WotC have mentioned, Ki will be partially inspired by Wuxia and fantastic martial arts, and that is almost entirely unrelated to the elemental magic that Rokugan Shugenja use.
Besides, Fighters may not be from the "I like swords" power source, but the Martial power source really isn't very far off. Most Martial classes are built around using weapons
very well, and little else. Similarly, most Arcane classes are built around throwing around fireballs (and other spells) very well, and little else. Power Sources tend to be very focused. It is because of that focus that a distinction between Ki and Martial is even possible, let alone the distinction between Divine and Primal, or Arcane, Shadow, and Elemental. If Power Sources were broader in focus, then it would be incredibly difficult to justify having more than an extremely limited number.