Translation:Do not enter the kitchen!
The idea that made you ask is correct, though there are two important notes here. Your example (before you edited it) with they-it would actually be luvutpa' and so couldn't be confused. You just happened to pick the one third person-third person example that uses a prefix. Your corrected suggestion of "before he cooks it, do not enter," would indeed also be written as vutpa' yI'elQo'.
The other note is that this should actually only be a problem in writing. This course does not teach stress accent, but in this example, for the noun, the stress should go on the last syllable of the root (vutPA') and for the verb, the stress should go on the root itself (VUTpa'). So even without context the difference could be noted in speech.
Okrand himself ignores the stress rules of The Klingon Dictionary. Listen to Conversational Klingon or Power Klingon and hear for yourself. I feel confident he'd pronounce vutpa' kitchen and vutpa' before he cooks it identically, with stress on the pa'. Basically, he always stresses a syllable ending in a glottal stop. The actors whom he coaches on the various Star Trek movies do the same.
The Klingon Dictionary, Section 1.3 (p. 17 in the paper copies). It reads in total:
Each Klingon word of more than one syllable normally contains one stressed (or accented) syllable. The stressed syllable is pronounced at a slightly higher pitch and with a little more force than the nonstressed syllable(s).
In a verb, the stressed syllable is usually the verb itself, as opposed to any prefix or suffix. If, however, a suffix ending with ’ is separated from the verb by at least one other suffix, both the verb and the suffix ending in ’ are stressed. In addition, if the meaning of any particular suffix is to be emphasized, the stress may shift to that syllable. Suffixes indicating negation or emphasis (section 4.3) are frequently stressed, as is the interrogative suffix (section 4.2.9).
In a noun, the stressed syllable is usually the syllable right before the first noun suffix, or the final syllable if there is no suffix. If, however, a syllable ending in ’ is present, it is usually stressed instead. If there are two syllables in a row both ending in ’, both are equally stressed.
Finally, it should be noted that there are some words which seem to have variable stress patterns, with the stress sometimes heard on one syllable and sometimes on another. This phenomenon is not yet understood. The rules given above do not account for this variability, but if they are followed, stress will wind up on acceptable syllables.
In the system used to transcribe Klingon in this dictionary, stress is not indicated.
That last line is true for this course as well.