have a knowledge of

Macmillan: "Knowledge is sometimes used with a, but only in the pattern a knowledge of something (or a good/deep/thorough etc knowledge of something):"

1 Kings 9:27 KJV: .. shipmen that had knowledge of the sea.." also 2 Chronicles 8:18 KJV

The usage seems to be an exception.

I found this on a WordReference forum:

"Besides bringing out a certain aspect of the notion denoted by the noun the indefinite article also has a stylistic effect making a description more vivid. Therefore the use of the indefinite article with abstract nouns is characteristic of the belles lettres style:

He was filled with a loathing he had never known.
He scanned her face: it expressed a dramatic eagerness.
Looking back upon that luncheon now it is invested for me with a curious glamour."

Learning to use articles by L. Barmina

http://forum.wordreference.com/threads/indefinite-article-with-abstract-noun-a-loathing-he-had-never-known.2734150/

I don't think this is so rare really. Other (perhasp less literary) examples from a couple of other websites:

There was a certain coldness in her attitude towards me.
I feel a certain reluctance to tell her the news.
Some children suffer from a fear of the dark.

Incidentally, 'a knowledge of' seems to have been much more common in the past, according to Ngram peaking arund the middle of the 19th century. As for justification, would 'he has knowledge of Latin' sound any better. Not for me it wouldn't (but I would be much more likely to say 'he knows some Latin' or 'his knowledge of Latin is quite extensive' or some such - the phrase as put sounds somewhat old-fashioned to me). What's more, the use of that indefinite article often goes hand-in-hand with an adjective, for example, 'a thorough knowledge of', where the article would, I think, be necessary. Other adjectives used like this include 'certain, good' etc.

in specifying learning outcomes of some university course what is better to write:
a student has knowledge of linear algorithms
a student has a knowledge of linear algorithms
a student has the knowledge of linear algorithms