The protest need to be aimed at parliament.
While laws are prown to interpretation. Interpreting the laws parliament passes is all the power the court has. Parliament is responsible for wording laws that force their planned interpretation.
To prevent this requires the sovereign parliament, to word the law in a non questionable way.
The only way this gets fixed. Is to convince parliament to change the GRC law ro clearly state that sutch operations make the recipient legally the sex chosen. And to address the intersex issue by stating such people are the sex they identify with as an adult.
The actual science only matters if parliament chooses to make it so. Even then the law tends to apply to the science at the time of passing.