Has the Scythe ever been used as a weapon?

There were scythe swords. They were a scythe blade attached to a sword hilt. Here's a picture of one.

TL;DR: The Hussites were famous for using flails and sang during battle, and so a possilbe inspiration for Hugo. This is not really relevant to your question about scythes, but may shed some light on how this passage you quote came about:

One was noticed who had a large, glittering scythe, and who, for a long time, mowed the legs of the horses. He was frightful. He was singing a ditty, with a nasal intonation, he swung and drew back his scythe incessantly.

The Hussites, a religios and movement that faught the Hussite wars, where known for thisbattle tactic: They fired with cannon and crossbows from the cover of carts until the enemy was in diasarray, then hussite infantry with pikes and flais would attack. It was alleged that they would sing church dittys while bashing knights with their flails. The hussites founded their own tradition of religos singing. That the Hussites sung while fighting may be hyperbole, but according to German wikipedia at one battle their enemy ran away because of the intimidating songs - or so one story goes.

So maybe Hugo heard of the Hussites and their battle songs, decied it to be a cool detail for his story and exchanged one farming implement for another, taking some artistic license.

Just to add to the accepted answers above, fencing master Paulus Hector Mair (16th Century) produced a treatise Opus Amplissimum de Arte Athletica on a wide range of improvised or unusual weapons, including the Scythe.

Yes the Dacians used this type of weapon frequently and it is very similar to a scythe. This is from Wikipedia so take from that what you will, but I have read about it in Roman history books as well I just dont have them handy at this moment, but to quote wiki:

"The most important weapon of the Dacian arsenal was the falx. This dreaded weapon, similar to a large sickle, came in two variants: a shorter, one-handed falx called a sica,3 and a longer two-handed version. The shorter falx was called sica (sickle) in the Dacian language. The two-handed falx was a polearm. It consisted of a three-feet long wooden shaft with a long curved iron blade of nearly-equal length attached to the end. The blade was sharpened only on the inside, and was reputed to be devastatingly effective. However, it left its user vulnerable because, using a two-handed weapon, the warrior could not also make use of a shield. Alternatively, it might be used as a hook, pulling away shields and cutting at vulnerable limbs."

Edit: After the OP added the condition of middle ages or later, I did find one source of the English Peasants Revolt of 1381 where the farmers/peasants armed themselves with axes, clubs, scythes, etc... and engaged royal forces. So this is one case they definitely used a scythe as you described as a weapon.

"On May 30, Thomas Bampton and two serjeants-at-arms went to Brentwood to inquire into tax payments and to collect any money due. Thomas Baker, the spokesman for Fobbing, informed him that they had already paid and had a receipt from Bampton. They would not pay again. Bampton became angry and threatened the men of Fobbing, but they had gathered with the men from Corringham and Stanford: no one would pay. Bampton's men tried to arrest the 100 men, but a mob drove -the three out of Bampton and back to London to report the incident. There were simultaneous uprisings on both sides of the names as peasants raised their scythes, axes, and knives in this "battle worth fighting...Between May 31 and June 1, the men of Essex gathered at Brentwood, Baddow, and Colchester. By this time the news reached the king, the revolt was under way."

source: Philip Lindsay and Reg Groves, The Peasants' Revolt 1381 (London: Hutchinson & Co., 1954) 20

link: English Peasants Revolt of 1381

Also found was the German Peasants Revolt of 1525

"While there were exceptions, the majority of conflicts were fought with scythes, axes, flails, and other farming tools. The League was also at an advantage by having armed hors*m*n, who could cover long distances much faster than a marching peasant army. Altogether about 100,000 peasants and sympathizers either died in combat or were later executed during the Peasant War of 1524–5. Many survivors were tortured and lost their privileges and property. Cities and villages that aided the revolts lost their rights; their weapons were confiscated"

source: German Peasant Rebellion, 1525 by Simone Cezanne De Santiago Ramos