I finally came up with a possible reason: the French word for organic is biologique, the middle part of which bears a decent phonetic similarity to 有機.
This may not be as far-fetched as it might initially seem. The Chinese word for latte is 拿鐵 (nátiě), which is a purely phonetic conversion. Perhaps something similar occurred for "organic", from the French word for it?
Update 1:
Alternately, the definition of 機關 (jīguān) is "organ", but that is in the sense of an organization/office, so it's not related to this meaning of organic, but perhaps whoever came up with 有機 mistakenly thought it did?
Update 2:
A native Cantonese speaker suggested that 有機 in Cantonese was chosen as being a decent phonetic match with "organic", further pointing out that Hong Kong would have been a natural place where Chinese language equivalents were created for foreign words. This idea seems to be the most reasonable explanation.
Update 2:
A native Cantonese speaker suggested that 有機 in Cantonese was chosen as being a decent phonetic match with "organic", further pointing out that Hong Kong would have been a natural place where Chinese language equivalents were created for foreign words. This idea seems to be the most reasonable explanation.