Pehaps I was not clear on what I meant when I talked about "science". The core of all science is the scientific method. There are general theories and special theories (ex: relativity) which serve as paradigms, and stick around as long as they are an effective description of reality as we know it. But the core of science is the process by which those paradigms came to exist, which, again, is the scientific method.
So, really, I don't see our two views as opposing. In fact, you just gave a perfect example for what I was so poorly trying to describe. In the throw you spoke of, I would teach the student that the throw will work, but against certain opponents. Against larger opponents, I'd probably tell her to concentrate on vital areas. But she would still learn the throw, because it is applicable in other areas.
This is still all very scientific. It's based on what would work for that student. (I'd also like to point out that the concept of a "set science" is actually counterintuitive to the very nature of science.)
But there are certain knife defenses that really don't work, and could get people killed (and don't get me started on gun defense). I grew up in bad areas, and carried a knife on me at all times as a necessity. I joined the Army and really got to know about pistols, rifles, and knives, and I have seen many knife and gun defenses in different martial arts systems and become very doubtful in the effectivenes of many of them.