The very notion of freedom of speech is a bit bizarre, as is freedom of religion. Sure, those things, like all other actions, should be mostly free. But why should speech (or religion) be so free that you can do whatever you want with no regard to consequences? We don't treat any other actions in that way, and yet we still generally want people to have a wide choice of actions they can freely pursue.
Some examples of "free" speech that most people might find objectional and that should probably be illegal to say:
The location and identity of people in witness protection schemes
The recipes for easy to make chemical and explosive weapons, and where to deploy them in, say, Sydney, to cause the most destruction
The location and identity and exact operations of undercover military or police operatives
Passing off the work of others as your own (plagiarism, intellectual property theft)
The private details one discovers about clients/patients that they don't want shared
Clearly no one should want people to be able to say whatever they want at any time with no consequences. Slapping "religion" as the cause of your actions should be totally irrelevant to how they are judged (not that it is unusual for the religious to use special pleading to excuse their own harmful behaviour).
If a surgeon described in detail on twitter, let alone took and published photos, the anatomy of a patient they had unconscious in their care, that would be both professional neglect and criminal neglect so severe you would expect professional and criminal sanctions. No one would be arguing for their freedom of speech (except maybe them and their lawyer). If the person defended themselves by saying they were just being truthful, as their God commands, no one would think that adds in any way to their defense, and clearly neither "free speech" or "religious freedom" are under threat from sanctioning this surgeon. If GoFundMe refused to let that person raise funds for a legal defense, no one would batt an eyelid.
The Folou case is much more nuanced than this, but the principles of "free speech" and "free religious expression" do not grant him automatic immunity. The harm of what he says has to be balanced against people's general rights to act freely provided they don't harm others, and clearly Rugby Australia felt the harm to them was higher than the consequences of not letting an employee have general freedom to do as they wish. And now it seems a court will decide if that was reasonable. But we are talking about relative goods weighed against each other, not absolute rights that trump all other concerns.