Honestly, it doesn't matter if the religion itself is against witchcraft--their are witches and magick in every single religion. Prayer in itself is magick, so is any mass, "puja" (hindu ceremony) or ritual performed for spiritual purposes.
Hinduism in general is VERY much like witchcraft in the fact that they have personal altars, some hold daily rituals, they chant mantras, dance sacred dances, pray, and overall, most if not all of their spiritual work is done at home. So I could see them co-existing very well.
Magick practioner deamed "bad" from any religious culture would be killed/hunted just like any other suspected criminal. Back then there was no difference in judgement between hurting someone physically or with magick. But ones who practiced for reasons deamed as "right" were and still are highly respected. Look at priests, priestesses, ministers, rabbis, medicine men/women, shamans, etc.
Of course, when politics mix with religion, sometimes those who are deamed bad were just labeled as such as an easy way to get rid of them. The witch trial hysterias were (in my opinion) just an abuse of power that went horribly bad. Now the damage done has become imbedded into the very fabric of many modern mindsets.
Overall I find hinduism to be one of the most open minded of all religions. Although I think you would need to ask someone who fully practices it (those in India not those anywhere else). Those in India know the beliefs completely.