What are the best support runes for punishing aggressiveness from enemies?

aery, because you can do damage and at the same time help adc with shielding, because yuumi, janna, sona, rakan, can shield, but when you play soraka or zyra you can do a sustain, or even burst dmg with those two champs.

Bone plating op asf in lane if u think ur gonna get harassed a lot

If your playing those champions and are not the aggressor your doing something wrong.

zyra rakan aside: Summon Aery 2,3,1 for mini runes but you can go 1/2/2 for shield+movement or 2/2/2 for mana+movement, - Resolve bone plating+revitalize. Bone plating is simply overpowered in raka/sona's position, and the revitalize boosts their healing and shielding even more. These are pretty much required even though Riot would have you believe it's simply an option. AP/armor/armor, AP/MR/MR or AP/AP/armor depending on matchup. Consider their magic pen or armor pen out of enemy support/mids here.

Zyra: Electrocute 2,1,2 for mini runes. -Sorcery you can play with. I'd say manaflow band / waterwalking, but you can go both movement speeds. One again consider enemy armor/magic pen when you choose stats. AP/AP/armor is probably a little better for Zyra, but if they pen a lot take AP/Armor/Armor or AP/MR/MR. I don't know about Rakan, he can go resolve for the extra shielding when hit by enemies, he can go damage on dashing to enemies or he can go aery. I don't play him so idk what is best.

If your problem is simply having issues with staying alive, then stuff like Bone plating comes to mind, as well as simply opting for tankier starting stats.

If it's really about punishing aggressiveness however, Presence of mind from the Precision tree comes to mind. A lot of enchanters (and in your case, all champions you play) have very powerful ultimates and being able to refund a part of it's cooldown every kill/assist is very useful, especially with how easy it is to rack up assists on them. Couple that with Transcendence and you'll find that your ultimate is very often up when you need it.

If you do go that way, I usually pick the Legend: Tenacity rune as second rune. Fully stacked it gives you 30% tenacity, which is pretty useful if you're scared of being picked off from deadly CCs. Alternatively Cut down can be used if you like being more aggressive.

Doesn't guardian also work well? Shield + haste makes it good for either forcing an engagement w/ advantage or ups the success rate of disengaging.