Well, of course. Freedom of speech is essentially the best corrective we possess as a species for making progress in whatever realm it may be, technological, scientific, ethical, or philosophical. Some of the issues that religion tackles are some of the most important philosophical questions that face mankind. Where do we come from? Why are we here? What's the meaning of life?
The idea that certain ideas, because of the fact that they invoke the supernatural, would be off limits could potentially impede that progress.