The will of the people is not always right or legal. A majority of Southerners were for slavery in the 19th century. A majority in many individual states wanted to continue legal discrimination too.

This is why we need the courts. Discrimination against a certain group is often supported by a majority of the voters but that doesn't mean it's right or moral.

By siding with the courts decision Arnold is upholding the separation of powers that the founders wisely put into the Constitution. The judiciary interprets the law and it is the executive branch (in this case the Governor) who enforces the law,