Here is an Ngram chart across the period 1700–2005 for "is an anathema" (blue line), "is anathema" (red line), "was an anathema" (green line) and "was anathema" (yellow line):
As you can see, the two forms without the indefinite article before anathema are far more common than the two forms with the indefinite article before anathema—and have been so for more than a century.
But an equally interesting Ngram chart compares "an anathema" (blue line), "anathema" (red line), and "anathemas" (green line) over the same period:
It is not at all surprising that the blue line for "an anathema" is always below the red line for "anathema," since any instance of the former is necessarily also an instance of the latter. But the frequency of "anathemas" (the green line) is markedly higher than the frequency of "an anathema," even though it is simply the plural form of "an anethema."
The few style guides I checked that discuss anathema at all seem not at all concerned about the issue of whether an indefinite article should precede it. The entry in Bergen Evans & Cornelia Evans, A Dictionary of Contemporary American Usage (1957) focuses entirely on the question of what the plural form should be:
anathema. The plural is anathemas or anathemata, not anathemae.
And Webster's Word Histories (1989), despite devoting a full page to the word, never discusses the sometimes-present, sometimes-absent indefinite article at all, referring variously to "an anathema of oblivion," "offered up as an anathema," "Among the more famous anathemas," and "the mutual anathemas" and quoting Deuteronomy 7:26 in the Douay Bible as saying
Neither shalt thou bring anything of the idol into thy house, lest thou become an anathema, like it. Thou shalt detest it as dung, and shalt utterly abhor it as uncleanness and filth, because it is an anathema.
and yet observe, in the next paragraph,
All of the church councils since the Council of Nicaea [A.D. 325] have worded their dogmatic canons to include the sentence "If anyone says ... let him be anathema."
It's as though the book doesn't notice the shift from "an anathema" and "anathemas" to article-less "anathema"—or doesn't consider it important.
And yet dictionaries identify all of the meanings of anathema, whether presented with articles or without them, are treated as nouns. The American Heritage Dictionary of the English Language, fifth edition (2011) makes this clear through its choice of examples to illustrate the different definitions:
anathema n., pl. -mas 1. A formal ecclesiastical ban, curse, or excommunication. 2. A vehement denunciation; a curse. "the sound of a witch's anathemas in some unknown tongue" (Nathaniel Hawthorne). 3. One that is cursed or damned. 4. One that is greatly reviled, loathed, or shunned. "Essentialism—a belief in natural, immutable sex differences—is anathema to postmodernists, for whom sexuality itself, along with gender, is a 'social construct'" (Wendy Kaminer).
As presented above, definition 4 gives no hint as to why anathema appears in Kaminer's quotation without an article. And yet in the quotation anathema reads as though it were a stand-in for an adjective such as monstrous or disgusting. None of the reference works I consulted explain how this split in treatment arose, although it may very well go back to translations of the "let him be anathema" wording cited by Webster's Word Histories from the Council of Nicaea and subsequent church councils.