The legislature can change the rules of how the initiative process is done, like they're doing here and tried to do last month with a bill that would've greatly increased cost for signature gathering while exempting unions—that was too far even for Brown.
They can't change what has been done via initiative without a further vote of the people or, as we've seen, via the courts.
Not sure that the courts would agree if it appears to be an attempt to stifle the process.