I do agree with the broader point, which is that there is something we could broadly call a "culture of free speech," and the Church was certainly not in favor

I do agree with the broader point, which is that there is something we could broadly call a "culture of free speech," and the Church was certainly not in favor of a culture of free speech. However, on the specific point of what got Bruno in trouble with the Church, it was definitely with regard to his theological ideas. Debates on whether or not there were other worlds and beings living on other worlds were a popular subject among academics back in the Middle Ages. In fact St. Thomas Aquinas had taken the other position, namely that no other worlds existed, and the Church condemned his argument as heretical because they interpreted him to have said that God could not have created other worlds, which would place limits on God's power. Again, none of this is to excuse the Church's persecution of Galileo, Bruno, or any of the other figures cited in the blog post you cite. Making a great intellectual discovery, scientific or otherwise, always requires some break with the conventional wisdom, and figures who are willing to do this in one area are likely to do it in other areas, too. Even if they happen to be wrong on many of these other fronts, they're following their train of logic to wherever it leads, and if you cut off those trains that produce socially inconvenient truths (think Newton's experiments with alchemy or his work on hermeneutics), you risk losing their ideas that turn out to be correct.