Equal Protection is the way to go: The Due Process argument, although more eloquent and perhaps more compassionate, is the tougher row to hoe. If you say the law violates due process, then you have to say the conduct is not illegal, which, as I love to say, puts the rabbit in the hat. Equal protection is better because many of these laws only go after homosexual conduct, and let the man/woman sodomy go all night...so to speak. That is more compelling, because then, you are not just criminalizing the conduct, but the very "persuasion" of being homosexual. I think that stands up better than Kennedy's rationalizing that in the 1500s, buggery meant a crime against children. But, that's just one man's opinion.
P.S. O'Connor seems to hang her hat on the "moral disapproval" issue - that being it's not rational to create a law just because you disapprove of a class of people in general (as opposed just to their conduct). I'm not sure that's true exactly, but I get where she's going. She's objecting to a sort of thought police - where the government looks into your mind and heart before you do anything, and criminalizes your desires. It's important because it smacks the Santorum/Scalia logic back to the pool of stupid ideas where it belongs, i.e. "I have nothing against homosexuals, just everything they do and stand for."