I'm working on a big chapter about religious freedom and freedom of speech. I've spoken and written on aspects of this before, but mainly in the Australian context. Most of what I'm coming up with now is new material, and a lot of it is based on case law from the European Court of Human Rights, which has developed a rich jurisprudence in this area. It's becoming apparent that there could be a whole book in this topic, but if so it'll have to wait for another time.
I do think that a lot of people (sometimes including the ECHR judges) tie themselves up in unnecessary knots finding conflict between freedom of religion and freedom of speech. The simplest way to understand them is as negative rights against the state. The state can't persecute you on religious grounds and it can't shut you up because it doesn't like what you're saying. In some cases, these freedoms can overlap (e.g. if you're expressing an unpopular religious message, as required by your religion's canons of conduct for its adherents), but they can never be in conflict.
But of course there can be a conflict if freedom of religion is somehow construed as freedom from criticism by fellow citizens, or as a positive right to call on the resources of the state to shut them up if you don't like what they're saying. I reckon we should resist that sort of interpretation. The real historical evils that led to modern ideas of freedom of religion related to state impositions of preferred religions and persecutions of dispreferred religions. Getting rid of those impositions and persecutions should be enough. After that, it's every idea, religious or otherwise, for itself.