I don't dispute any of what you say; in fact, I think perhaps even not just a topic for the 'educated' but also in more popular venues.

But the context here was Cromwell talking about (hypothetically) preferring to allow 'Mahometanism' to be practised in England, not just as an idea or social construct of far-away others.

Since there wasn't any great likelihood that any legal or social changes were going to actually cause 'Mahometanism' to suddenly flourish in England, it is indeed a pretty easy throw-away remark.