Have atheists ever been persecuted in India? Wikipedia article on persecution of atheist has nothing about India, and google did not throw up anything useful.
How does Carvaka count as Hinduistic? There are atheist-but-not-rationalist nastik schools of Hinduism which deny gods but accept the Vedas as uncreated, which can be called Hinduistic atheism, but I don't see how Carvaka can be pushed into the Hindu fold.
As for what Indian religions consider valid -- "religions" cannot consider, only people can consider, what people consider has varied widely over time. In contemporary times, both Vaisnavism and Saivism are generally considered part of the Hindu fold, but Vaisnavites and Saivites persecuted each other for centuries (Ramanujan being an infamous example). There are saffronist attempts to include Jainism and Buddhism within the Hindu fold, but both those communities were persecuted by kings in hock to Brahminical religion (as Gnanasambandar gurgled with joy over).
In any case, to answer the original poster, I don't think the historical record as we have it now shows persecution of individual atheists (in the contemporary sense of atheist) but the historical record barely shows any atheists at all. In contemporary times, there has been persecution of atheists, see the stories about Sanal Edamaruku being run out of town.