The idea that free inquiry is needed for the advance of science is one of the quainter and more naive myths of the enlightenment. Attached to it is the common misconception that science took off in Europe when the grip of the Church was loosened.
In the academic world there is a newish discipline called the Sociology of Scientific Knowledge (SSK for short). SSK made itself deeply unpopular with scientists because it insisted on studying them and not simply assume that they were objective and disinterested. This approach has taken some flack from the usual opponents of 'postmodernism' but it remains important because the questions it asks are good ones. The biggest question is "How do scientists do science?"
Getting back to the question of free inquiry, it was long assumed that if you put a lot of clever people to work without any strictures at all, they will produce something useful. We now realise that they won't. The problem is not that they won't think of anything, it is that they will think of everything with no way of telling the good ideas from the porkers. It's not my area of expertise, but I have long suspected that this was the problem with science in the ancient world - it was just too free and hence could never construct any linear research programmes. There was no authority to decide between Aristotle and Epicureus apart from everybody else's personal opinions.
What you need for science (and what we have today) is a strong, agreed authority responsible for training new scientists within the orthodox citadel and casting out heretics if they stray too far from the paths of righteousness. Thus, creationists, parapsychologists, Brian Josephson and most of the alternative medicine community are branded as heretics and excluded. And jolly good it is too, I say. I completely agree with this modus operandi of science even though, unlike most scientists, I see it for what it is. There is nothing much free about all this inquiry. Science sticks within orthodox methods and assumptions and thrives as a result.
What about the Church? True, this was the authority that once decided on orthodoxy and heresy. That power has now been taken over by science itself where it belongs. But science could only do this when it had already become sufficiently successful to become an authority in its own right. Before that, it sheltered under the authority of the Church and the result was largely benign. Magic, astrology, alchemy and the like were excluded from mainstream science. Theology was kept out of the question by forbidding natural philosophers to talk about it. Realist metaphysics was enforced. All in all, the Church was an excellent step-parent until science could stand on its own two feet. Then, like all adolescents, it started to rebel against its elders. Hopefully, now it is grown up enough to admit that it actually owes them a lot.
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