I think it's a bit confusing that you have to click the timestamp to get the direct URL. I suggest clicking on the message itself. (And yes, that means remove the pop-up feature.)
Is this because you don't like modals? What if we used URL rewrites so that modals changed to the correct URL for the post like Twitter does?
Changing the URL like Twitter does would help, but to me it seems better to load a new page. Keep the pages simple so that they load fast. You are doing an excellent job at this.
I support this idea. Don't mind the pop-up too much but it should maybe include context if it's a reply like Twitter does and show a little more of the thread/convo?