I think the best way is to improve Stone's Endurance.
I've got a few different ideas.
My first thought is to increase the number of times you can use it. Once per short rest is what they currently get, maybe change it to half proficiency per short rest. So, at higher levels it can be 3 times per short rest. Heck, might not even be to broken to just go straight to prof per short rest.... probably a little broken.
And, I think I like that more than making it prevent more.
Also, while resistance is going to do better some of the time, at low levels it is completely worse. 1d12+3/4 is going to average about 9, but it can easily do more. And, before level 5 getting hit for 18 damage in a single blow is pretty devastating. And, it isn't going to happen often, which is going to make the roll less valuable.
Though, getting the minimum sucks, so maybe add in a floor to the ability. It can't prevent less damage than your level? This does take it over past early levels, but it feels decent to me.