There is a known bug that happens where the intellect devourer will totally disappear IF you do the prison map LAST. Bioware is working on a patch for that but right now the only known solution to this issue is to use to turn on the debug codes and respawn a new intellect devourer.
If, however, you are doing this map FIRST (before blacklake, docks etc.), then reloading from right before you go in to fight him is the only solution i can offer.
SPOILERS to FOLLOW
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Just to make sure, did you talk the other guards into leaving before you attacked the Gaoler? If so, the intellect devourer will not be killed when the Gaoler is killed. Instead the intellect devourer will attack you in his normal form. Be aware that he has the innate ability to go invisible and may just be hiding. If you didn't talk the other guards into leaving, then the ID will jump one by one from guard to guard until you kill all of them as well. THEN you will have to kill the ID in his normal form.
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