Either "wɪnd" or "waɪnd" is acceptable, according to Dictionary.com, but merely being acceptable doesn't satisfy me. "Wɪnd" seems better to me, due to the connotation of blowing wind, etc, but apparently "waɪnd" is preferred, being listed first. Which was originally intended? (Or does it really not matter?)
According to the Oxford English Dictionary, the pronunciations /waind/ and /wihnd/ are used to indicate different verbs. They write:
The sense 3 that they give is:
So the wind in respects to a horn would be waɪnd.
If your question is: was wind (blow a musical instrument) originally pronounced like wind (wind up a clock) or wind (as in wind and rain), I believe the answer is both. Merriam-Webster dates this usage to 1586, shortly before Shakespeare started writing plays. William Shakespeare repeatedly rhymed wind (as in wind and rain) with find and kind, which I assume would also rhyme with wind (wind up a clock), as they do today.
The pronunciation has changed since, so the sonnet no longer rhymes.