The legitimacy of Indian courts is something only Indian citizens and people living in India can decide. Other people may have opinions, but they are more or less irrelevant.

Anyway, the fundamental issue here is that domestic rulings often have international consequences. As a sovereign state, India obviously has the right to ban the Wikimedia Foundation, or any other foreign entity, from doing business within the county. That right is an essential aspect of sovereignty. If they don't like you, they can ban you. But if the Wikimedia Foundation values access to India more than their right to host a particular article, they may choose to comply with the demands of an Indian court, even in matters where the court does not have jurisdiction. And that compliance would technically be voluntary.