The thought of alternative medicine contradicting science is merely based on ignorance. I see no relation whatsoever with creationism. Science knows how evolution and the creation of the universe occured, so it is valid in saying that creationism did not occur. It does not know how some alternative medicinal techniques can work, it still says they are not working. Do you see the essential difference?
Your view of everything having a naturalistic basis is dangerous. You create causality where there is a clear correlation. Causality is something very hard to prove. To me there is no point in saying that one or the other is the basis, they are all responcible and they should all be treated for an optimal result. Also keep in mind that the scientific knowledge of hormonal and electric signaling that occurs in our brains, which is your naturalistic basis, is in a very very early stage at best. In other words, we haven't even begun to comprehend how a minimal change can affect who we really are or what all is possible.
Which brings me to your second point ... who says that energy has no mechanism? I'd claim it has a very distinct mechanism. In the orient the knowledge of the energetic body has existed far longer than our western medicine. It's been studied, shared and investigated by so many people who dedicated their lives to it. A system that everyone agrees on has been developed, which has been worked out in great detail. Then that knowledge seeped over to our world and from our scientific view we turned a system that makes complete sense to so many into 'magic'. That's exactly the bias I've been talking about in my previous posts. Eastern medicine is simply written in a different language, that of meridians, chi and chakras. But over here they tend to take it all literal, instead of trying to translate it into a western scientific viewpoint. It's the same as reading the bible literally, instead of seeing it as a book about morals.
I know there have been some studies that suggest that the chinese meridian concept, which lies at the basis of accupressure, accupuncture and a lot of other eastern medicinal methods, does have a physical mechanism. Most of the accupuncture points lie on highly innervated locations in the body. Meditation and accupuncture, heck even massages have been shown to cause widespread physiological changes, not only in our brains but throughout our bodies. Alteration of the magnetic body, that is created by our electric and ionic processes, by use of strong magnets have been shown to cause changes in our physiology. Many possible explanations have been hinted at, none really investigated in depth.
Take it from me, Parallo, the scientific community is very biased and, just like the larger community, it has trends. These trends ensure that science moves in a certain direction and everyone who wants to go in a different direction will usually be 'destroyed' by sheer peer pressure, not always because there is no proof .. but often because their peers do not want to see the proof. This is why I am confident that alternative medicine can become scientific, if the community only drops it's bias and really tries to investigate how it works. I'm not naive enough to believe that this will be happening any time soon though.
Also like I already said, not all alternative medicinal practices are good in my eyes. There is a lot of 'fraud' going on because of the lack of regulation. I'm a cynic too

But a cynic who keeps an open mind and does not discard something based on a lack of knowledge.