Flexibility in Japanese written forms
Written Japanese has two layers to it -- the words as pronounced, and the words as written. This double-layering allows authors to play around with nuance in ways that just aren't possible in other languages, like 月光【ムーンライト】 or 巾着【さいふ】 or 紅葉【はっぱのはなび】.
熄【や】み in specific
Your example isn't quite as much of a stretch, as や(み) is actually one of the recognized kun'yomi for the kanji 熄. See also the entries at WWWJDIC or at the Japanese Wiktionary. Note that this is a so-called 表外字【ひょうがいじ】 or literally "off-the-chart character", as it is not included in the list of 常用漢字【じょうようかんじ】 or "general-use kanji", and this character is therefore somewhat rare.
In terms of nuance, 闇【やみ】 refers to "darkness", while 熄【や】み brings in shades of "ceasing, halting, disappearing".
Etymology (word origins)
Both terms reflect a root verb yamu meaning something close to the 熄 sense: "stopping, extinguishing, disappearing". This is related in turn with words like:
- 止【や】む: something ongoing stops, such as the rain
- 止【や】める: to quit doing something, such as annoying your sister :)
- 辞【や】める: to resign, to quit, such as a job or post
- 病【や】む: to suffer from something, to become sick (probably from the way that sickness often led to someone stopping their normal routine, and possibly even "stopping" completely, i.e. dying)
- 病【やまい】: disease, sickness
- 病【や】ます: (archaic) to afflict someone, to inflict something on someone
- 闇【やみ】: darkness (from the way the light extinguishes or disappears)
Learning the root forms can open up all kinds of related terms. I find that my understanding of Japanese is much richer when I learn the connections and associations between words.
This root yamu may be related to the term 黄泉【よみ】 for "the underworld, the land of the dead". In the oldest texts, the word also showed a combining root reading of yomo. The entry at the English Wiktionary states that this may be an ablaut (vowel-shift) relative of 山【やま】, from the way that mountains were associated with the dead in ancient times. That entry has no sources listed for this derivation, but the sound-shift alternation //a// ↔ //o// is apparent in various other terms rooted in ancient vocabulary, where //a// seems to indicate "outward" and //o// "inward".
(Full disclosure: I've edited that 黄泉 entry. However, I did not add that particular derivation.)
Anyway, make of this last part what you will. :)
Please comment if the above does not address your question.