Interesting topic, and something I've thought about often. Although I've never really studied Karate, I have seen numerous videos and read several articles on the similarity between certain kata movements and qigong. This is also the same in various Kung Fu styles, most notably White Crane. Seeing as how some Karate styles (like Goju) are said to descend from some form of White Crane, I think it makes sense that there are qigong aspects to Karate as well. Something as basic to Karate as horse stance, is a very powerful qigong movement, used for building body connection.
I do think that these movements were inserted to heal the body from imbalances and injuries that might occur during fighting or sparring. However, it should be noted that to practice the kata as a healing movement, one would have to be taught the basics of intention and leading qi, at least as far as I am concerned.
I also beleive that these movements are there to build a 'soft body' and to strengthen/build what are sometimes called 'internal connection.'
Other arts also have qigong movements 'hidden' within the technique. Many Aikido techniques, for example, are qigong movements. I'll never forget my astonishment when a Chinese qigong teacher had us perform a solo Tenchi Nage (Heaven and Earth Throw). I asked him if this came from Aikido, and he laughed and said he had only heard of Aikido, never seen it.
The main thing here, from my experiance, is to find a teacher who understands this level of the kata/technique, and is willing to teach it. If not, studying qigong from an outside source might be an option, so that you can bring that knowledge into your practice.
"Seek not to follow in the footsteps of the men of old; seek what they sought."