I tried Unison before and gave it up. Not because it is not a great software. But because two way sync itself is very dangerous in my eyes. If I made some stupid mistakes in one side, my all data gone.
I've been considering treating each directory as a separate version control target, so that the archive server would never lose anything. I have the same qualms - although so far, Unison has worked perfectly for me, even in cases where in retrospect that surprised me.