No one has claimed that "every Catholic alive at that time loved the Inq! They had a thing like All-Star voting, and people voted for their favorite torturer!" The thing existed, was monstrously evil, and trying to minimize the evil of it backfires with many people. Even if the Inq authorities had, and strictly adhered to, a 15 minute time limit that anyone could be tortured, I'm not impressed.
That is an important point. It's just as important to say that most catholics today would find it abhorent. But they don't have one lick to say in what the church does because unlike the Biblical model, the clergy doesn't answer to the Body of Christ.. UNLESS as in the pedophile scandals of recent history, the US government leaned on the Church and the congregants stopped paying tithes - all of a sudden, Rome was all ears. They still foot dragged, and so on; but, they at least began to look concerned enough to do more than shuffle people around, cover up and let it continue elsewhere.
Scripture tells us that our ministers are to be judged on their message against that which was delivered by Christ and the Apostles - period. Paul said that even to the extent that if he should come preaching another Gospel, the congregants should curse him. Not the clergy, the congregation! He wasn't speaking to the southern baptist convention of ministers, he was speaking to the church congregation. The clergy did wrong and the congregation did nothing to stop it of any measure and were rather complicit.. but as if they had any choice. The clergy in the Roman church isn't of them, it is over them. That isn't biblical. The clergy answers only to itself up or down and the Pope essentially answers to no one. That isn't scriptural. It may be Catholic; but, it isn't scriptural.
Killing people over their sin isn't scriptural under the new covenant either. These are the Christian lessens to be learned - they haven't been and in fact are utterly rebuked by the Church as anti-catholic.
From a purely practical standpoint, there is no remedy here that I can see.