I suspect when they wrote the laws in they needed some boundary requirements. It probably depends on how they wrote it. If they had no concept of being gay, then they probably wrote it as "one man and one woman required" without much more thought, or even realizing the possibility that people can be gay. If they were equipped with modern biology and knew that gay people are born that way, and that they constitute 5-10% of the population, things may have turned out different.
On the other hand, interracial marriage probably was not even a concept 200 years ago because-despite the existence of black non-slaves-the very idea that all people are equal was still barely a social norm. Even most abolitionists did not think that Black people were equal, just that we should not have slavery.
I agree that most things should be legal unless proven otherwise, but there are some things we cannot predict about what standards should apply in the future. As an example, in the future if lowering the age of legal adulthood occurred and is considered obvious and just, then marriage laws would have to be rewritten to accommodate. It isn't necessarily our fault for not being able to foresee this.
This all leads up to what I believe is the greatest strength of our legal system and constitution (or any constitution), is its ability to change and be flexible. Passing amendments (however unlikely in our current polarized political arena), courts striking down laws, etc. The ability to rectify the situation based on new-found experience. The guys who wrote it knew we would encounter problems and situations of which they would have no clue about, and changes would have to be made.
One one hand there exists dumbfuckery, and on the other there exists the fact that we do not know what will or will not be socially acceptable in the future. There are some things banned right now that I think are dumb, because I have put lots of thought and argument into those issues and seen evidence that supports my conclusions. There are probably also plenty of things that I cannot even fathom to be unjust that may only become obvious over time as social constructs change and technology progresses.