Jisho

This is actually ateji. In other words, the し in しごと originally comes from the stem of the verb する. So しごと would literally mean "what one does." Then, the kanji 仕 was chosen because it has a related meaning and can be read し as well. It did not originate as a onyomi-kunyomi compound. This technically also makes it a jukujikun, in the same way that 時計 is a jukujikun.

Er, scratch the part about 時計 being jukujikun. It's ateji, but not jukujikun.

And, sorry for the triple post, but there are many words that have mixed or exceptional readings. On-kun, kun-on, gikun, jukujikun, etc. So it wouldn't have been that crazy for it to be on-kun, but it just happens to be jukujikun.

There are really many many words that are read on-kun, kun-on or kun-kun. Not everything is on-on.

場所 (kun-on)
潮風 (kun-kun)
晩飯 (on-kun)
... just to give you an example.

I have one question. What is gikun and jukujikun? I've heard of kun and on before though.

Gikun are non-standard readings using the meaning of the kanji to express some kind of idea. For instance using the kanji 寒 (meaning cold, used in the word さむい) with the reading ふゆ (winter, typically written using the kanji 冬). That would be a gikun reading. These are most often seen in fiction, employed by creative writers.

Jukujikun are more common. Many common words are jukujikun. Basically, it means "a kunyomi reading that has been applied to a set of kanji rather than only one." Some examples include 大人 (おとな, adult), 今日 (きょう, today), and 可愛い (かわいい, cute). The core concept of kunyomi readings is that they are originally from Japanese, from the time before kanji were used. The same applies to jukujikun, but they just happen to be written with multiple kanji.