Left hand is used a lot and right hand hardly ever in non-lethal, so primary and secondary is arguable...
Agreed, I almost never use the sword. But the sword stil
feels like the primary. Same thing for me in Thief, I almost never use the primary (sword or bow, only for shooting water arrows when needed). So even if I use secondaries much more they still feel like secondaries and it therefore makes sense for me.
RTS games are the same, much more right clicking than left clicking; it still feels right. What it all comes down to is prefference and what you are used to. My guess is that most people who feel to use right click for right hand in this game is people who are used to how things work in skyrim