Your San Francisco is showing
If you scroll to page 55 of the following pdf you can see the statement Thomas made. You will be hard pressed to find him saying that same sex marriage should be repealed.
To me, this is a great example of how lazy our press have become. Thomas appears to mainly be saying that he (and Alito) think that the issue of same marriage should have been taken up via the legislative branch, which would typically include some accommodations for religious liberty, while also avoiding stigmatizing those with religious beliefs that run counter to the notion of gay marriage. His point seems to be that the court is the wrong venue to address this issue, not that same sex marriage should be repealed.
But it's way easier and will drive more clicks to say that Thomas and Alito want to repeal same sex marriage. Sad.
At this point I just want to see the source documents and I heavily discount the commentary around it from all media outlets. They almost all suck at this point.