Remove Runes that give damage
The way I see it, if Demolish was removed Sion wouldn't be initing to victory by building full tank. And you wouldn't be losing half your HP to a single ability without the runes that stack on damage for things like dashing, being in river, hitting someone with an ability. Rewarding just playing the champ with more damage.
There is no way to balance them either without drastically altering champs that are optimized around them. The best thing to do is to remove them next preseason and either try to be more creative with runes so they don't just stack damage onto champs mindlessly, or to just remove them all and balance champs to be good without them.