Proposition 22 was an initiative to change the law, not an initiative to amend the California Constitutional. That was a big mistake by the proponents of Prop 22, but they were probably trying to cut corners on the cost, since it requires a lot more signatures to place a Constitutional initiative on the ballot.
So the San Francisco controversy still revolves around the wording and meaning of Article I, Section 7(b) of the California Constitution:
A citizen or class of citizens may not be granted privileges or immunities not granted on the same terms to all citizens. Privileges or immunities granted by the Legislature may be altered or revoked.If the courts interpret this section to mean that marriage must be open to gays (i.e., "on the same terms to all citizens"), then Prop 22 is irrelevant, since that state Constitutional provision overrides any state law or legislative initiative.