If I understand you correctly, I don't disagree, but would observe that finding a such a right protected by the 9th amendment at the time it was passed, is going to take a heap of diggging, and probably will result in a dry hole. Sure the federal government had no power to legislate in the area at all, but you'd have to find someone who argued for such a right, or a provision in state constititutions or laws of the time, or even in English Common law, protecting such a right. It's not like the application of privacy rights, to internet communications, where one must ask the question "what would the founding fathers do" in applying the Constitution to such a situtation. They knew about homosexual acts, the state and before that the colonies had laws against them. They also had similar privacy protections to those of the 4th and other amendents, in their state consittutions. Those can be looked to. What can't be looked to in order to interpret the US Constitution are the provisions of the European Covenent on Human Rights, which is in part what the court did. The 9 th amendment protects rights "retained by the people", which to me says those rights had to be recognized as rights, not made up 200+ years later, and in part by an extra-consitutional foregin body at that.
You are correct in that States had laws outlawing homosexual behavior. And prior to the passage of the 14th Amendment, those laws were unquestionably Constitutional. There was not, to the best of my knowledge, any Federal law on the matter. And indeed, the 10th Amendment would forbid any instrusion into what was a State matter. As I said, there is arguably a Federal "right to buggery" contained in the 9th Amendment. That 9th Amendment right is now protected from State infringment under the 14th Amendment.
(Cases like this make a good argument that the 14th Amendment is perhaps too broad. But as I said before, I'm torn on the matter. I live in California. While I want Sacramento writing laws for some areas of life, I don't want them writing gun laws. I'd much rather have the 2nd Amendment protecting my rights than the nebulous "right to self-defense" in the CA constitution. I hope to see the 14th Amendment used one day as a blunt instrument on CA's gun laws!)