While it makes sense that the Japanese, whose primary initial contact with Europe was the Dutch (mostly Protestant and recently independent of Catholic Spain) bought into Dutch propaganda regarding Catholicism and how the Church functions as an organization — inquisitors of the Church did not use torment as punishment. The inquisitors of the Spanish Crown sometimes did, on the basis of a non-Catholic being a traitor to the throne, that said such things wren't nearly as wide spread as is generally supposed, and the harsher actions of the Spanish Crown were opposed by the Church.
The Church's goal in Inquisition is to convert as many as possible and correct the perceptions of as many heretics as possible, so obviously going the route shown here was not a thing on their end. Any member of the clergy who tried would be promptly punished themselves, thanks the Church's abilities as an organization — not all religious organizations did half as well, and religions without an organization got the Thirty Years' War.
Many heretics involved themselves with treasonous groups and it was on account of the treason that they were put to death, often in horrific ways, by the government of whichever country was in question. (And thanks to a remarkably stupid move by Pius V, English and Welsh Catholics were always suspected of being treasonous for hundreds of years — quite possibly the biggest reason Catholicism became uncommon in Great Britain. Like I said, remarkably stupid. And a complete violation of the separation of church and state declared by Jesus in Mark 12:17 and Matthew 22:21 — since Catholicism wasn't actually outlawed ever on the Isles.)