The will of the people is the Constitution of the United States of America, not a ballot measure passed by a slim majority of California voters, nor any other ballot measure passed in any other state. The judge determined that the will of the voters in California violated the rights of a minority guaranteed by the federal Constitution. Those rights were equal protection under the law as guaranteed by the Equal Protection Clause and the right to Due Process. The law is written, "No State shall make or enforce any law which shall abridge the privileges or immunities of citizens of the United States; nor shall any State deprive any person of life, liberty, or property, without due process of law; nor deny to any person within its jurisdiction the equal protection of the laws."
Supreme Court precedent holds that marriage is a fundamental Constitutional right...
Taylor versus Safely (1987): "the decision to marry is a fundamental right" and "marriage is an expression of emotional support and public commitment."
Zablocki versus Redhail (1978): "The right to marry is of fundamental importance for all individuals."
Cleveland Board of Education versus LaFleur (1974): "This court has long recognized that freedom of personal choice in matters of marriage and family life is one of the liberties protected buy the Due Process Clause of the Fourteenth Amendment."
Loving versus Virginia (1967): The "freedom to marry has long been recognized as one of the vital personal rights essential to the orderly pursuit of happiness by free men."
The right of marriage is the right of two parties to choose a spouse, and with free and mutual consent, join together and form a household where they then consent to support each other and their dependents. If polygamists or any other "alternative lifestyles" wish to argue that the state has an interest in promoting marriage that includes more than two parties or other factors outside this definition, then let them. They must provide evidence to support that they can provide just as stable homes as heterosexual couples and same sex couples. It has been more than adequately demonstrated through evidence in this case that same sex couples are just as capable of providing a stable household and raising children as heterosexual couples. There is no evidence to support that polygamists, pedophiles, etc. are similarly capable.
The judge defended the will of the people, the federal Constitution; by overturning Proposition 8, which sought to mandate gender roles and restrict same sex couples to a culturally inferior institution by excluding them from marriage and the cultural dignity, respect, and stature inherent in marriage. The state has no interest in excluding one group from a fundamental right without rational basis and so the judge was obligated to overturn it.