First of all: I never understood (and never will understand) the “scientist” hype around Giordano Bruno (especially when Johannes Kepler was only younger by 20 years; it's not like there was no other available hero in the same period). Bruno's thought is completely unlike everything produced by modern science. His cosmology happens to be comparable in some ways to the results of modern science, but his method is esoteric, speculative, and is in many ways spirituality more than science. In fact, pre-modern cosmology was mostly philosophical musings about “what the universe should be according to abstract principles,” and Bruno was still a representative of this medieval and Antique mindframe.

Though I have studied this period as an undergrad, it is not my academic speciality, so someone more competent than me will certainly be able to correct or precise my answer. A first problem is that the Inquisition never was a unified body—there were several inquisitions, at several places and several times. But I will assume we are speaking about the modern, and the medieval, inquisition and especially about the Roman one, that has sentenced Giordano Bruno. What can we say of it?

• Was the Inquisition an attempt to regulate behaviours? Yes, certainly—one amongst others, it must be noted. The history of the Church can, in many ways, be understood as an attempt to curtail behaviour and to impose its moral and social model (and the Early Modern one was particularly concered with it). That being said, the same can certainly be said of the State. Was it sometimes unfair, did it cause suffering? Undoubtedly, as is usually the case when people face institutions. I agree with /u/Maklodes that Bruno's case was certainly not a model of fairness, and that the non-scientific nature of his thought does not make his execution fairer (but it does change the picture presented by people who pretend that Church = obscurantism).

• Was it especially cruel? No. Torture was a standard procedure to (i) obtain confessions and, sometimes, (ii) to inflict punishments, and inquisitors were no more prodigal at it that secular justice. Overall, though it is not without exception, the Inquisitions conformed far better to our modern standard of efficient justice than most states of the period—they had procedure rules, trained judges, and a universal jurisdiction (in Spain, they were often used by the central power to infringe on local privileges; something that was overall less successful in Italy), which does not mean that they were perfect Kelsenian judges, but still (by the way, someone mentioned witch-hunting—outbreaks of violence against witches happened mostly on the western border of the Holy Roman Empire, in areas of religious cohabitation. No relation with Spain or Italy).

Overall, I think that we tend to make far too much of the Inquisition, which is very much a product of its time, and has nothing especially aberrant (except for the success of Protestant propaganda against it). According to people who have integrated as an axiom the rule of law, yes, they were not models of fairness—but precisely, 16th century Europe had in no way integrated the rule of law as an axiom, which makes this kind of retrospective judgements completely pointless.

PS: and to distribute “gold stars,” since it was the point of the original question after all, I would say that Cosmos and the Catholic League are equally misguided in this case

Much like historians of genocides, holocausts, dictatorships, and the like, historians of heresy and inquisition have a tough time finding an approach to these subjects which isn't moralizing and judgemental. And we have to avoid moralizing because the historian's work is not to judge events for the lessons it can provide (which is subject to interpretation), but to understand the events, peoples, motivations as they were (not as we hope them to be). The reader can then make their decision as to how to judge. As such, I can't determine for you or anyone if the inquisition was 'as bad as it's made out to be' because:

1. I don't know what you know about the medieval, renaissance and early modern contexts of Christian behaviour and attitudes, of 'law and order' and of corporal punishment

2. I dont know what you conceive of 'as bad as it's made out to be'

So, I want to help readers approach this subject through several aspects in order to come to their own conclusions not only about the inquisition, but how to understand the complexity of the subject and how it is used, both by the television show Cosmos, and by the editorials/calls to action of the Catholic League, and often by Redditors. We have to understand what is heresy, what is the inquisition, and was there a conflict between science and religion.

In the last 24 hours /r/AskHistorians has had many question provoked by the new Cosmos, and here are some things I've written to consider:

Carl Sagan's Cosmos and his history?

How dangerous was being a heretic?

How did one become an inquisitor?

Very recently, there are two other relevant posts which get into the Conflict Thesis, the so-called (imaginary) battle between Science and Christianity:

How common were witch burnings in the middle ages?

[How common was it for someone in the Medieval period to be to be executed for proposing hypotheses about the natural world that didn't line up with the perspective of the Catholic Church?] (http://www.reddit.com/r/AskHistorians/comments/1tsrvu/how_common_was_it_for_someone_in_the_medieval/cebs5i4)

The question, then, of how bad the inquisition was depends on your relationship to expressions of authority and power. But here are some facts:

• the medieval, Spanish, Roman, and Portuguese inquisitions were different in formulation and construction, and they exercised specific powers which sometimes were in common and sometimes diverged

• these inquisitions, much like most interrogations of heresy, were often less about theology than they were about power, and in Foucault's words, control and discipline

• the medieval inquisition, and the Roman Inquisition, were still guided by a principle of 'returning sheep to the flock': the evidence makes clear that recanting heterodox and heretical views led to lenient punishment (perhaps a pilgrimage to a local shrine, or requirements to attend mass and confession with exact frequency)

• latter inquisitions did use torture, developed over time

• all inquisitions did engage in corporal punishment and execution, and those would not have seemed out of place on the battlefields and in the courts outside the doors of the self same churches and places of inquisition