Let's dissect it for you.
Quote:
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Cardinal Ratzinger was head of the Inquisition, the arm of the Church set up to investigate, persecute or eliminate heretics.
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Cardinal Ratzinger was head of the (Holy) Inquisition (comma, which indicates the end of a phrase). This is indisputed, feel free to do your own research at catholic.org.
Next part:
the arm of the Church set up to investigate, persecute or eliminate heretics. As already explained, this refers to the office of the Holy Inquisition and why it was created.
Do not assume it means that Cardinal Ratzinger personally is responsible for the persecution and elimination of heretics. This is where your simple mind fucked up, and made you look like a fool for speaking among your superiors.