So he's asking for a degree of accomodation of particular groups' own religious or moral code, and clarity about how that accomodation works. Plus he's pointing out that this is already a problem, ie taht the secular state is intruding further on this than it used to. (link
The Archbishop wants to distinguish between uninformed prejudice, cultural habits, and religious scruples. He suggests that the last of these should have a status in law which the other two do not, and that an appropriate religious authority can make the distinction in ways that would command "a high degree of community recognition".
On the first suggestion: I don't have the knowledge to agree or disagree with the Archbishop's comments on Islamic scruples, but I would be very doubtful if scientology or voodoo (for instance) were accorded the same status.
On the second: being from a free church background, I tend to react against the idea that some group of experts has the authority to decide whether what I believe is really basic to my faith or merely a cultural habit/uninformed prejudice. I might personally be prepared to concede that role, for this specific purpose, to some group of leading church figures like the Archbishop. But I'm sure that some of my fellow Christians, on some issues, would not. Think for instance about teaching creationism as science in schools; or homosexual practice. The Christian community includes people with strongly held but opposing views about what our faith means for these questions. I don't see how any authority could retain broad support within the community if it was called upon to decide whether scruples on these issues are really rooted in our faith or not. I suspect the same difficulty will arise for Islam. (link
I find I fundamentally agree with what he says, and also with how he expresses it. I can see the incensed reaction to how his comments have been reported. I dont see what in this speech as he wrote it is threatening or offensive to self-confident and right-minded people. (link