i feel a urge to post a picture of Fluffy, destroyer of worlds.
What is so much worse about actually destroying a planet vs all of the standard planetary invasion options such as planetary bombardment/core detonation that cause the planet quality to drop?
Nobody gives 2 shits about you nuking a planet from 20 to 2 quality, which lets be honest is practically the same.
Why should you get a massive penalty for the one but the other is just business as usual in a war? Perhaps we also get cool stuff like supergerm warfare or something to attack planets.
Aside from that, why only negative penalties? Why wouldn't a malevolent race praise your show of force? Why would civs that fear you/are much weaker publicly denounce you instead of becoming more afraid?
Such acts could perhaps also give a morale boost to malevolent civs, and only penalties to benevolent. Or perhaps benevolent would require more checks an balances before resorting to such acts whereas a malevolent could just do it because they feel like it.
Maybe United Planets can be involved: ussualy they only have a "ban superweapons" thing, but perhaps if there is alot of malevolence in the galaxy, they can decide that if a war drags on long enough, a drastic measure is needed to end it and sanction the use of a superweapon.
I feel a lot more could be done with this then just a penalty.