Having JUST read a hefty amount of your comic recently, you're fine. Gunhild never came off as a Mary Sue due how much she happens goes through throughout the journey.
The only thing that changes this is the situation with the runestones... I can see why you might worry then. Technically, they were earned by reliving a sad memory. It's not the same as earning them through some arduous task, and she manages to use them perfectly well the first time using each. Everything else that happens to her outside of that is still impacted by what she decides to do in a given situation.
All in all, you're sort of on the line between having a Mary Sue and not having one. The battles are where I'd suggest making rewrites. The easiest way to avoid writing Gunhild out to be a Mary Sue while keeping the same exact story is.. have her get hurt more in battle and/or struggle to learn how to use the runestones.