I am following the algorithm for obtaining a braid from a link as explained on pages 23-24 here: https://math.berkeley.edu/~vfr/jonesakl.pdf.
If I let the axis run straight through the center region bounded by the trefoil knot, then it is already braided. If I choose a counter-clockwise orientation, I get that the braid word for the trefoil knot is $\sigma_1^{-1}\sigma_1^{-1}\sigma_1^{-1}$ rather than $\sigma_1\sigma_1\sigma_1$.
Choosing the clockwise orientation, I get the correct $\sigma_1^3$.
Is there a canonical choice of orientation (perhaps clockwise)?
No, there is no canonical choice. Alexander's theorem is an existence theorem, but it is very far from a uniqueness theorem. In fact, there are many, many, many noncanonical choices in this construction:
Varying these choices will produce infinitely many possible braids.