Halachically is ש a single letter with two pronunciations or are there 2 different letters in the Hebrew alphabet (shin and cin) which happen to be draw the same in the torah, have the same gematria etc. For example if the wrong letter is used in a legal document would the document validity be in question? Or if a scribe writing a torah intends to write a cin instead of a shin for God's name (sha-kai).
Torah, mezuzot and tefillin, or legal documents are written without nekudot (vowels). This includes the dot of the shin/sin. So there would be no halachic difference, being that there's no difference of the letter.
This is only for writing. When praying, reading the Torah, etc., you'll need to say it correctly.
Edit: I just realised that you wrote 'intends' for the Torah. I never heard of a sofer needing to know how the word is pronounced before writing it. As long as he writes it correctly, and his intention is l'shem mitzvah, I don't see why there should any problem.