Yes, the pronunciation would differ.
qet be' is two words, so you have word stress twice.
qetbe' is one word, so there is only one word stress, on the suffix with the apostrophe.
It's a little like the difference between "a black bird" and "a blackbird" in English -- one has two word stresses (on "black" and "bird") and the other only has one (in this case, on the first syllable of "blackbird").
We don't actually know enough about how Klingons stress syllables to declare these differently pronounced. A Klingon who wanted to make it clear that qet be' was two words could say them slowly and separate them, but it's quite possible that in normal speech one would only be able to distinguish qet be' and qetbe' through context.
i give 'the woman run' as an answer didnt work
Indeed. "the woman run" is not currect English.
If you are talking about one woman, it has to be "The woman runs." with an -s on the verb.
If you are talking about several women, it has to be "The women run." with an -e- in the second syllable of "women".
If you are talking about one woman did yesterday, it has to be "The woman ran." with an -a- in the verb.
"The woman run." is never correct.