Unfortunately, just about any popular program or method of exercise today is saturated with either an Eastern religious approach or some other form of spiritualism; including a humanistic, self-centered approach to good health. This is because everyone recognizes that complete health must be that of body, mind, and spirit. We were made a trichotomy by our Creator, after His image, and it is hard to separate one part from the others. They work together. We, as Christians, should only be putting into our minds that which is holy and pure, and we believe our spirit can only be helped by the Holy Spirit who guides us into the truth of God's Word. Anything contrary to the Bible will not help our mental or spiritual health, even if it is beneficial to our body.
That being said, the physical aspect of various workouts such as Yoga or Pilates, etc. may be beneficial to our bodies... However, as many of these have a focus on flexibility, you may want to look up some of the research being done on the topic of stretching and how it relates to performance and injuries. There may be much better ways to increase flexibility than static stretching (stretch a muscle and hold for a period of time). As for other physical benefits of workouts such as yoga (strengthens breathing, provides stress-relief, increases blood flow, improves posture...), it is my opinion that just about any exercise (walking, running, cycling, weight lifting, swimming, rowing...) can provide most of these benefits equally, if not better than yoga.