I don't see your point. Men are allowed to marry the opposite sex. Women are allowed to marry the opposite sex. The most natural reading of the laws on marriage and their state Constitution is that equal protection requirements are met, even without considering that the primary definition (and until the recent activism the only definition) of marriage is the joining of a man and a woman. The proper route for changing laws that are constitutional is legislation, not litigation, and the gay-marriage advocates are undermining the rule of law by using the Courts to write new laws through dubious rulings.
If I wanted to marry my first cousin (and cute as she is, I don't), I wouldn't be able to do it legally in half the states. Is that an equal protection question too, or is it more properly in the realm where the legislature should be writing the laws? How are the gay marriage and incestuous marriage questions different constitutionally?
When a law contains exceptions based on gender, such as your formulation, “Men are allowed to marry the opposite sex. Women are allowed to marry the opposite sex,” it is no different from older laws that made exceptions based on race, such as “Black people are allowed to marry the same race. White people are allowed to marry the same race.” Many Christian faiths (where our “primary definition” of marriage comes from) still insist that marriage should be retained between two people of the same church: “Catholics are allowed to marry Catholics.” The last time I checked, our government was supposed to promote religious freedom, which also applies to gay marriage.