What was past is gone. Things change. It doesn't matter whether in ancient time martial arts had moral philosophies attached or not. It doesn't even matter if all the stories anyone has ever heard about the Shaolin temple are fiction. What are you doing now? Do you need to learn chuan fa and traditional weapons to protect your family and your town? Or to do your job, for employment? To go to war as a soldier? If not, then why are you doing it? These surely were the main reasons people wanted to know and develop martial arts in the past, when the myriad styles we have now were codified. Do you do it to preserve a family tradition, is it your heritage? Do you do it as a sport, to compete in contests? Maybe you practice because you have an interest in anthropology and culture, and want to do something that people of the past might have done.
The point is, martial arts are whatever we make them. No one can live in the past. Whether shaolin monks used martial arts as a form of spiritual practice or not...it's being done now. We decide what martial arts are.
"I am a servant of the Secret Fire, wielder of the flame of Anor. The dark fire will not avail you, flame of Udun! Go back to the shadow, you cannot pass!"