Here's you problem. No. They did better than that. They did better than any other court system in the world they could read about or experience. That's an important historical distinction from "they were doing the best they could."
These guys advanced the cause of human rights and justice. And to the extent they appear barbaric: that was the extent to which they were unable to rise above their times, not the extent to which they subjected their times to otherwise unknown hardship.
The Inquisitors did improve matters. On the other hand, the tools they devised were often inadequate. It is importsant to remember that our court system is medieval in origin, that the Common Law incorporates much of canon law, that our courts equitable jurisdiction comes directly from the example of the courts presidened over by clerical Lord Chancellors. But having sais that, it still remains that horrible injustices were committed, because even saints are fallible and are often so uncertain what to do in the face of evil that they end up doing evil. Let us learn from their bad example as well as by the good.