While the Church was initially thrilled at the potential for millions of converts, the Clergy and the pope himself quickly became disapproving of spains methods in conversion.

They particularly had a grudge with Slavery, the second archbishop of Mexico openly wrote letters denouncing the way missionaries were run and I'm sure you can find a million more examples of how the conquistadors were immoral and the clergy of the catholic church said something about it.

So in conclusion the Catholic church did denounce the practices but overall it wasn't serious enough for them to take direct action against it such as excommunication or various ultimatums on the treatment of native peoples.