Yes, Spanish priest Bartolome de las Casas tirelessly petitioned against the encomienda system, which allowed Spaniards to demand free labor from Native Americans. He depicted the atrocities against them which he'd seen as a Dominican Friar, and he argued that Native Americans should be converted to Christianity rather than exploited for labor.

His performance in court led to the enactment of the New Laws of the Indies in 1542, which was primarily known for abolishing slavery of Native Americans. It was not enforced, however, and many Spanish plantation owners simply argued that the natives were debtors, working off the "free" schools and infrastructure which the Spaniards provided them. Ultimately, friction over the New Laws and high mortality rate among Native Americans led the Spanish and Portuguese to seek alternative labor in the form of the Trans-Atlantic Slave Trade.

edit: Sorry, I didn't read your subtext regarding Bartolome. I think his success, limited though it was, speaks for itself. However, anything else I post would just be speculation.

Slightly related, Christopher Columbus and his brothers were imprisoned by the Spanish crown for their tyrannical reign. Columbus was said to have been brutal as he tortured, maimed, killed indigenous people without mercy during his reign as Governor. They were jailed for about a month and lost their power so, yes, it was frowned upon to an extent. It's similar to how killing/torturing slaves was illegal but at the same time, the law was rarely enforced.