yytz,
Although the Supreme Court normally uses the rational basis/intermediate/strict scrutiny framework it has not done so in Lawrence and Windsor. It has never held that homosexuals are protected group warranting special protection and it has never held that sodomy was a fundamental right. Rather Justice Kennedy has eschewed the normal framework for an inquiry focused on the motivation behind the law. If that motivation is soley or even primarily moral disapproval or animus then the law is invalid.
Alternatively put, moral disapproval is deemed by the Court not to be a “rational basis” and if that is the primary basis, the motivating factor, of a law that restricts people’s freedom then that law would be unconstitutional.
It is true that most prohibition express some moral disapproval, but those prohibitions will primarily motivated by other grounds, i.e. to prevent some harm that will come to someone or to create some efficiency.