Yoga is Hindu, but it is not religious. When Hindus go deep into the issues raised by the San Diego court verdict ("yoga is not Hindu"), they are bound to encounter some problems with their own tradition.
In my opinion, Christians who allege that Hindus mix up yoga with the worship of another supreme being than the jealous god Yahweh, have a point. And Hindus who think that yoga implies the worship of a Hindu god likewise have a point,-- the same point. But those are modern Hindus who talk a lot about yoga but are unlikely to practise it. Contemporay Hinduism is a lot more God-centred than the ancient originators of yoga, such as Patanjali, or even the late-medieval pioneers of Hatha Yoga. Ancient Yoga was certainly “Hindu” in any normal use of the term, but it was not theistic.
On Rajiv Malhotra’s discussion list, where the verdict is debated, one Hindu recently quoted Arya Samaj fouder Swami Dayananda Saraswati with approval as asserting that Yoga is “restraining all activities (vritti-s) of mind (chitta) from all evil and unrighteous affairs and fixing the same in God alone, for the bliss and beatitude is Yoga and disobedience of God's injunction and indulgence in evil thoughts and deeds is Viyoga, i.e., remaining away from God”. I am not sure about the exactness of this “quote”, but it gives the gist of Dayanada’s thinking, and it certainly renders the thinking of this particular Hindu and many millions of contemporary Hindus.
In reality, yoga is not about evil at all. It restrains good motions of the mind (i.e. thoughts) as much as evil ones. Hinduism is quite conscious of good and evil, but unlike Christianity, it subordinates this concern (on which the Christian core doctrines of hereditary sin and salvation are based) to the concern for Liberation. Patañjali defines yoga as “restraining the movements of the mind”, full stop. Dayananda’s additional considerations of good and evil, and especially his bringing in “God”, are typical of modern devotional Hinduism or bhakti. This very successful movement, which eclipsed the non-theistic trends in Hinduism (Advaita Vedanta, Sankhya, Mimansa, Buddhism), is the historical antagonist of Hatha Yoga. It teaches that Liberation does not mean “isolation” (of consciousness from its objects, Patañjali’s goal), does not mean identity with the Absolute, but aspires no higher than watching God face to face, much like Sufi and Christian mysticism. It also rejects the emphasis yoga puts on techniques. If God’s grace is there to help you, what use are techniques? By contrast, yoga means reaching the goal, Liberation, by means of techniques.
The trouble already started with the Bhagavad Gita. I have it on good Hindu authority, but I have also seen it for myself, that the Gita is a work of “synthesis”. Then already, Hindus were enamoured of synthesis. Thus, this is where we first find the notion of an equality between three disciplines: karma yoga, “the discipline of action” (then meaning Vedic sacrifice, now moralistically interpreted as good works), jñana yoga, “the discipline of knowledge” (meaning Upanishadic knowledge of the Self, i.e. yoga proper), and bhakti yoga, “the discipline of devotion”. In fact, when Yajñavalkya introduces the notion of the Self, he pits its knowledge against the Vedic rituals. The ancient Vedas and esp. the Brahmanas (the technical manuals of ritual) are centred on karmakanda, “the (ritual) action half”, while the Upanishads are centred on jñanakanda, “the knowledge half”. While yogis would simply choose the latter, the Gita proposes a synthesis, viz. the third pole, bhakti.
The book discusses a number of then-popular Hindu philosophies, but interjects in every chapter one sentence that does not follow from these philosophies at all, namely that all this shall be given to you if you are but devoted to Me, Krishna. You can read Patañjali’s Yoga Sutra, but you will not find Krishna there. You can read the Buddha’s teachings on meditation, but Krishna is not there. Yoga can perfectly exist without Krishna.
Modern bhakti Hindus project their own bhakti beliefs on the whole of Hindu history. They deny the reality of change (both progress and degeneration) in Hindu history. In fact, it is they who realize the Westerners’ fond image of Hinduism as frozen in time, unchangeable. So, they rewrite the theory of yoga as dealing with God. In fact, the more God, the less yoga, and the more yoga, the less God.