Gnosticism, for example, is obviously not pronounced with a hard g. As far as I know the modern English use of agnostic is said to have originated with Thomas Huxley, who surely would have been aware of the correct pronunciation.
Is there some odd rule or quirk that explains this? Or has it simply been repeated enough that people now consider it to be the standard pronunciation?
There is really no other way that it should be pronounced. The initial G in Gnostic is silent to avoid pronouncing the word "guh-nostic." But it is not the permanent character of the G to be silent as others have pointed out. When the sound is found mid-word, the G is always voiced as in such words as AGNOSIA, AUTOGNOSIS, COSMOGNOSIS, COGNITION, AEROGNOSY, BIOGNOSY, PHARMACOGNOSY, ASTROGNOSIA, ORYSTOGNOSTIC, PNEUSIOBIOGNOSIS, PROGNOSIS. And when similar Greek-rooted words are formed such as with gnatus forming COGNATE and PREGNANT.
Another example where the prefix a- awakens a silent Greek consonant: AMNEMONIC is pronounced am-ni'monik.
In Greek, the "g" is pronounced in the word "agnosis", so that makes me think that Thomas Henry Huxley, who created the word "agnostic" had knowledge of greek and just pronounced it with the "g" as it should be. The "g" is only not pronounced if not preceeded by a vowel.
The pronunciation of words that begin with ag- is stranger than I had imagined. According to Merriam-Webster's (which provides what it considers the main U.S. pronunciation for each one), very few such words are pronounced with the g attached to the same syllable as the a. To my surprise, Merriam-Webster's says that the a is pronounced as a stand-alone syllable—separate from the following g—not just in most words where the primary vocal stress is on the second or later syllable (like agree, aglow, and agave), but also in most words where the primary stress is on the first syllable (like agate, agony, aggravate, and agriculture).
In fact, the only ag- words (where the g has a hard "g" sound instead of a soft "j" sound) that Merriam-Webster's reports as being pronounced with a first syllable of "ag" instead of "a" are the agn- words—all of them, from agnate to Agnus Dei.
The dictionary's analysis seems counterintuitive—I spent the first two decades of my life around people who, I could swear, were pronouncing Aggie as though it consisted of the syllables "Ag" and "ee." But perhaps the dictionary's analysis is correct and relies on a more sophisticated ear than the one I use.
As for the question of why English speakers pronounce agnostic with a hard voiced g instead of as befits a word that prefixes gnostic (a word that has a silent g in English and good Greek roots) with the modern counterpart of an alpha privative, I ask in return why the citizens of Lafayette, Louisiana, stress the first syllable of their city's name and pronounce that first syllable as though it were the laff in "laff riot."
Isn't this simply a case of adding the "a" before the word to indicate 'not' or 'un' or 'non'. The base word, gnostic, means that something is known, or there is knowledge of. Placing the "a" before the base word implies that there is not knowledge of, it is unknown. I don't believe the root word is generally pronounced with a hard 'g' sound, and so adding the "a" before, the "a" should have hard sound. There are many, many words which have an "a" prefix added to indicate 'not' or 'non', especially in science and medicine.
As Aaron K says, typically we pronounce all the letters of a Greek consonant cluster when it occurs between vowels word-internally, even if there is a related unprefixed word with a "silent" initial consonant.
There are certain exceptions, such as words containing a vowel-final prefix before "-psych-" (parapsychology, antipsychotic), but agnostic usually isn't one of them. (The "pt" in the word "apoptosis" has been pronounced both ways, as /t/ and as /pt/.) As Aaron K mentions, there are other examples with the negative a- prefix, like amnesia; also apnoea/apnea and Agnatha.
The exceptions are mainly words where the division into "prefix" and base is still salient to a modern English speaker. Even though the "a" in "agnostic" is etymologically a prefix, I don't particularly think of the composition of the word each time that I use it (that is, I don't think "oh, 'agnostic' = 'not gnostic'").
I don't know if you can really answer a "why" question and there aren't a lot of "agn-" words to study, but the only other such word that comes readily to mind, "agnate", comes from the same process (ad- + gnātus), and is pronounced the same way.
