Then the issue isn't in the runes, it's in the new champions and item changes.
Regardless the true source, damage needs to be nerfed across the board. Perhaps an easy solution would be to just increase base and per level armor and mr for everyone?
So to be clear, if we're saying support Leona and support Nautilus do too much damage, and the only items they buy are Knight's Vow and Stoneplate, exactly how are systemic item and champion changes causing them to deal too much damage? Leona deals the same or less damage than she's done at any other point in her lifetime and runes are pretty close to neutral, too.
Now if your point is specifically Qiyana or AD Assassins are too good, then that's another discussion with different data and different history.