They're getting rid of most of the runes, and a lot of runes have basic damage increases, so they have to make up for that somehow. But I don't think that they want to nerf health because that would make certain already squishy heroes (Lux) be a lot worse than they otherwise would be.
But I think that the first patch once the new runes hit is going to be mega unbalanced in some way because it's a new system. It's just a matter of what kind of unbalance it's going to end up being. I guess Riot would rather it be unbalanced via damage instead of health. She says as she watches some tiny rune no one looked twice at, make some hero/item combos a menace.