Was it just invented by authors who found it a fitting term for birds so associated with death and ill omens? I can imagine it originating from an Edgar Allen Poe story. Does anyone know it’s true origin?
(And as an addendum to that, what are cats called again? A cacophony? Have any of these terms (or any that you see printed in the lists) ever been common in everyday language?)
“parliament of owls”, “committee of vultures”, “unkindness of ravens”, “pulchitrude of peacocks”?
There’s a few strange ones!
It’s not actually clear that it was originally anything other than a fanciful invention for one of those lists of wacky “group of __” term lists. Granted, the original such list mentioning “murder” for crows was in the 15th century, but there’s little evidence that the term was in actual use apart from such mentions. It was then repopularized by compilers of such lists again in the 20th century, from which any modern use stems.
(The Oxford English Dictionary describes it as “One of many alleged group names found in late Middle English glossarial sources. App. revived in the 20th cent.”)
BTW, the person who is responsible for reviving the terms (many of which were never in widespread use before him) was James Lipton of Inside the Actor’s Studio.
A clowder.
The handful of such usages are ones which native English speakers do not think twice about using. But when you think about it, why is it that cattle come in herds, while sheep like chickens are in flocks, wolves and wild dogs are in packs, lions are in prides, and kangaroos in mobs?
It should be a catastrophe of cats! 
On a humorous note (while we were waiting endlessly for the telco to repair a fiber circuit), my business partner asked me “If it’s a flock of seagulls and a pride of lions, what is the collective word for phone techs?”
“An embarrassment”, I replied. I used to be one, so I know…
I thought this was a joke based on the similarity of names at first, and then I looked it up, and, wow, you’re right. Fancy that.
A bit late for Halloween but here is the helpful Stoakes-Whibley Natural Index of Supernatural Collective Nouns for future reference 
I would’ve thought it was pretty self-explanatory - you see carrion crows gathered in large numbers, you know something’s dead. Though of course the fact that it’s a murder, rather than a freak accident of crows, may be for dramatic effect. Or it might just be that a corpse lying unattended outdoors, where the birds can get to it, is statistically more likely to have met a violent end.
Here are a lot more for you - a lot of these are ahistorical, fanciful and/or of interest only to pedants and Dopers. 
List of animal names - Wikipedia
And here are links to Wiki’s other lists of such collective nouns: http://en.wikipedia.org/wiki/Category:Lists_of_collective_nouns
While we’re adding new collective words, I really must insist on this one: “a conspiracy of women.”
Murder does make sense for crows given their scavenging nature. I’m sure more than a few farmers found the bodies of farm animals killed by predators by looking or listening for crows.
“Most of the [following] expressions have appeared anonymously in Word-lore, 1926-28, Vol. 3, No. 2: 54, 60, and No. 5: 132. Others have been added by JAMES LIPTON in An Exaltation of Larks, New York, 1968, and by HAL BORLAND in the Audubon Magazine, Vol. 71, No. 1: 46-47, 1962; a half dozen more were found in WRIGHT’S English Dialect Dictionary and a few in JACKSON, 1968. In these articles most of those expressions appear to have been taken to be society names. It is not always so, however…”
(This is a quote from a voluminous work by yours truly)
A moderation of Dopers?
Anyone who has heard them will appreciate the collective I invented: “a caucus of crows”. Or maybe it should be “cawcus”.
Or maybe a “cowcus” of cows, a queer of steer, and a Biden of gaffes?
In modern parlance, all these terms have been conveniently replaced by “shitload”.
“A pride of lions” is one of the only more fanciful collective nouns that is still commonly used, referring to the regalness of the King of Beasts.