In all fairness to the two churches that banned yoga classes in the UK, the 'banned classes' were being held in the church facilities. The churches did have the right (and dare I say responsibility) to draw a line between what they considered practices in keeping and not in keeping with their faith, as they see it and want it presented. Since their name is on the front door of the building, they are responsible for the religious content of whatever happens in the building.
As far as teaching yoga in schools, if they are public schools, then any teaching for Physical Education classes should be stripped of religious content, be it Muslim, Hindu, Christian, or Buddhist.
Yoga does have undeniable Hindu religious roots. While yoga can be taught without these elements, it usually isn't. Shakra points, prana circulation, and the like are Hindu concepts devoid of physical education value, and shouldn't be included in classes taught in public schools.
What concerns me about the fatwa in Malaysia is what I see as a general trend in Islamic countries: freedom is not extended to allow any disagreement in personal belief or practice. Freedom of conscience is an alien concept, and individuals are not credited with the ability to tell the difference between right and wrong. Therefore adherence to public moral standards must be maintained through heavy-handed external controls. This shows up in persecution of religious minorities, be they Christian, Jewish, Hindu, Zorastrian, or Sufi (groups persecuted to varying degrees in all Muslim countries where they live). I believe this comes from a different baseline belief about the nature of Almighty God Himself - Islam portrays Him as an arbitrary totalitarian authority (hence the belief that governments should exercise this same level of authoritarian control), while the Judeo-Christian view sees Almighty God as a loving Father (who therefore gives worth and value to each individual and allows the exercise of free will, even to the point of allowing the individual to make bad choices). I may not personally believe in the Hindu roots of yoga, but I would lay down my life to defend your right to believe and practice it.
