Food for thought
If you think broadly about Shioda Soke's definition of Atemi - "whenever you make contact with focused power [this is Atemi]" - then you could restate it as ‘intentionally directed energy at the point of contact', and for the sake of simplicity I'll limit the point of contact to the physical domain. Applying the broader definition to Aikido we find that all techniques are Atemi, and the seeming controversy over the application of Atemi in Aikido becomes an argument for which technique is appropriate for a given situation. Hence, which of the three ‘Atemi' is appropriate should be rather straightforward given the specific circumstance, personal belief systems not withstanding. In this way we can see how Aikido is Atemi used in harmony with a situation, instead of viewing it on the surface as merely ‘striking' or some other pugilistic connotation. Again, this is just an application limited to the physical side of techniques. I don't mean to suggest here that Kiai and Aiki are one and the same, as they are obviously complimentary.
Actually, given the variable of ‘contact', inductive logic yields an even broader definition -- ‘ Intentionally affecting [the energy of] some other system ‘ - such as a training partner for instance. The notion of intention brings us back full circle to the difference between Aikido and ‘Striking' Martial Arts, although I would say that many seek to achieve balance/harmony as well.
If you think about this carefully, you will find that what appears to be very different on the surface - the differing Martial Arts - are in fact connected in deep ways.
Anyhow, these are just some of my thoughts on the subject -- it's just food for thought.