I'd like to point out why there's an article here.
In Swedish, with professions and similar things, you usually don't have an article.
He is a lawyer. = Han är advokat.
However, when you're using words like this more figuratively, you add the article.
He is a clown. = Han är clown. = It's his job.
He is a clown. = Han är en clown. = He behaves like clown.
The same is true here. gudinna is not a job of course, and the person in the sentence is not really a goddess. So you can't take the article out of this sentence.
And how would it work with monotheistic/polytheistic religions? If a goddess is one of many, could one then also say "Hon är en gudinna" or would one still remove the article?
And now I come to think of it, in English we phrase it differently if the speaker believes in the god or goddess in question. "He is God" only for my own god (if I had one); whereas "he is a god" could be used both for my own and for some generic god.