Sorry to drag up an old thread, but I have a contribution to make
I am a Bujinkan Budo Taijutsu practitioner (ie. Ninjutsu) in one of the apparently few dojos in the world which actually trains hard and for realism. I can understand why your perspective is that "Most of Ninjutsu is bull", Chconcerned.
I am a Christian and have been for pretty much my entire life. I have been practising in the Buijinkan for about four years now and have, of course, been exposed to utilising energies. To me, this is a very real thing and is very easily demonstrable when you observe or practise Sakki tests. This is where you sense an attack coming from outside your field of vision. It is also interesting to experience first hand the effects of an attack being made with energy and intent behind it, not just physical strength.
I was skeptical at first of the spiritual aspects of Bujinkan, however through my own thought and study I came to my own conclusions which are easily demonstrated.
A couple of examples - If you enter a room just after there's been a fight, even if there is nobody in the room and you were unaware of the fight occurring, you can still 'feel' the negative energy. Likewise, if you walk into a room full of people truly enjoying themselves, you can feel the positive energy.
This is something that is inherent in all of life. Animals are especially attuned to energies and it helps to drive their instincts. If God enabled the animals of the world to feel and use these energies to their advantage, then why can we not do the same as human beings?
Getting back to my point, it is important to separate the concepts of a religious belief behind spiritual aspects of a martial art from the spiritual aspects themselves. I no longer believe that manipulating, feeling and using energies is sinful or wrong in any way (except when the practise is used to sin) as it is an integral part of how life functions. As always, of course, it is important to always put God and His commands to you above all else.
If God tells you to leave a martial art, either to take up another one or to no longer practise any art at all, then you are obligated to obey Him.
And don't forget that Christ told His disciples to carry swords to protect themselves from thieves and bandits. In today's society, life is no different - possibly worse.
In my eyes, my being capable of defending myself and my loved ones is a greater show of love than many other things. My sacrifice of time and capability to put myself in the firing line in order to keep my friends and family safe from would-be attackers to me is very important. If I failed to prevent someone from being killed when I know I could have prevented it, I would feel I had sinned through my inaction.
That being said, you can prevent someone else by sinning through being able to control them. What if you have a drunken relative who starts throwing chairs around the place in anger? Obviously you wouldn't want to hurt them, but if doing nothing puts others at risk then it is important that you are able to restrain this person.