You are right to recognise a joke.

As you might tell by my username, I'm an admirer of Gibbon (and seventies British comedy). His actual historical work is, perhaps, not useful to someone who wants to learn about the Romans- but that is not so much a reflection on him as it is to how much more vibrant the field of classical history is in the twenty first century. Archaeology, newly available ancient texts, innumerable new perspectives from innumerable new scholars: the field has moved on.

I'm not a classicist however, so I'l leave that thought there. Nor will I attempt an explanation of Gibbon's impact on, in particular, history written in the English-language.

But what I do think has lasted very well in his work is the sheer quality of the prose. Anyone who has spent time in an academic library knows that many of the most brilliant scholars do not not know how to write pleasingly. This is, to some extent, an aesthetic judgement, and it is important to note that historians and other scholars of the humanities have just as much right to use technical jargon and dense language as any other intellectual. We would not judge a quantum physicist for writing a book for her fellows in the field that was not understandable by the general public; historians must be allowed the right to communicate complicated ideas in dry prose when necessary.

Gibbon, though, was and is funny.

Gibbon was a figure of the late British Enlightenment; and like several other thinkers of that time and period his works were less than devout. A useful comparison might be to David Hume: it is not so much that the philosopher was an atheist or an agnostic, but that he was irreligious and aware of the absurdities of organised religion. Hume, in his*Treatise on Human Nature * famously wrote that 'errors in religion are dangerous; those in philosophy only ridiculous.

Like Hume, Gibbon was writing for an elite audience in the 'Republic of Letters,' men and women who often balanced nominal Christianity and shows of faith with a witty skepticism of established dogma. The example par excellence might be Denis Diderot, whose Encyclopedia's entry on Cannibalism famously ends 'See Eucharist' This was before the French Revolution made atheism seem part and parcel of a murderous threat to property and the lives of property owners, of course.

In the quote you cited, Gibbon deploys one of his favorite devices: irony. You'll note that he does not deny that the Pope was the vicar of Christ, or that the religious dispute was a serious one. He simply places those 'more scandalous charges' next to the grotesque crimes of 'piracy, rape, sodomy, murder and incest' and allows the reader to note the incongruity.

Here's another example, in one of his best footnotes. (I have yet to find any historian since Gibbon who has written better footnotes.) This is in Chapter Fifteen of The Decline..., 'Progress of the Christian Religion.'

According to the canonical gospels, as Christ died on the cross, there was a miraculous portent when the sky went black across earth. (Luke 23:44, 'And it was about the sixth hour, and there was a darkness over all the earth until the ninth hour.') Gibbon expresses absolute amazement at the fact that such a dramatic event occurred and yet no one else seemed to notice.

Here's his quotation:

Under the reign of Tiberius, the whole earth, or at least a celebrated province of the Roman empire, was involved in a preternatural darkness of three hours. Even this miraculous event, which ought to have excited the wonder, the curiosity, and the devotion of mankind, passed without notice in an age of science and history. It happened during the lifetime of Seneca and the elder Pliny, who must have experienced the immediate effects, or received the earliest intelligence, of the prodigy. Each of these philosophers, in a laborious work, has recorded all the great phenomena of Nature, earthquakes, meteors, comets, and eclipses, which his indefatigable curiosity could collect. Both the one and the other have omitted to mention the greatest phenomenon to which the mortal eye has been witness since the creation of the globe. A distinct chapter of Pliny is designed for eclipses of an extraordinary nature and unusual duration; but he contents himself with describing the singular defect of light which followed the murder of Cæsar, when, during the greatest part of a year, the orb of the sun appeared pale and without splendor. The season of obscurity, which cannot surely be compared with the preternatural darkness of the Passion, had been already celebrated by most of the poets and historians of that memorable age.

Note that that entire passage is written, as it were, with a straight face. The gospels said that this happened, says Gibbon, so we all know it must have happened, right? Isn't it bizarre that people acted like it didn't happen?

So, to sum up, when you say

Was this comment intended as a joke, or did they really reflect Gibbon's/contemporary society's view of religious offences as much more serious than secular charges?

The answer is: Yes, it was a joke. But it also reflected the view of his contemporary (elite, literate and literary) society. Gibbon's audience were receptive to, and in on the joke.