I am not a Hindu nor do I practice Yoga so my knowledge and experience with chakras is minute, but what I do know is that I can always feel a difference when I work with them. As far as I have studied and experienced cultures from around the world all have some chakra like system from the Daoists, Qabalists, Bard's, et cetera.
I agree that people should study and experiment with whatever they find of interest or are called to do, but before they try and remove something that is considered a vital force of their (and every living creatures) very existence, I would suggest deeper study and praxis into, as this example, chakras, otherwise just leave it alone. Leave it all alone - psi, magic, yoga, qigong, metaphysics. The practice of magic and mysticism is not a game because it can cause very real damage within your visceral and psychological self and the world around you if proper care is not taken.
Removing chakras, to me, is like removing a vital organ. You don't want your Muladhara? Well, it was nice to know you genitals!