There are a great many morally repugnant things that used to be the norm in our society: colored only bathrooms and drinking fountains, anti-miscegenation laws, sundown laws, and even slavery. We've done away with most such nonsense and our society is better for it. Because we've expanded who is rightfully entitled to the basic human dignities enshrined in our Constitution to include more and more people who when left to the tyranny of the local majority end up marginalized by unjust laws and customs.
The debate over same sex marriage is just the most recent battleground over the expansion of who else gets the rights most of us already enjoy. And just like the previous battles over civil rights, we as a society will expand the coverage of those rights to include people who might be different in some way from the majority but still ought to be entitled to the same basic protections and privileges of the law.
That has been the trajectory of our society and its relationship to civil rights. Moreover, far from being an unacceptably evil series of developments, this has been a morally good thing and a justifiable source of pride to later generations who get to live in a more just and fair society. And who if they consider something in all of this to be evil would apply that label to those who bafflingly (perhaps violently) stood in opposition to equal rights on the wrong side of history.