I know there already is a topic about the antimatter card, but this topic is about the effect, since antimatter isn't just limited to the card, but purple nymph and pandemonium can cause the effect too.
I have a simple suggestion, cause a negative effect creature to be effected by shields as though it were a regular attack. So a shield that reduces damage by 2, would reduce negative attacks healing by 2, too, creatures with negative attacks can be poisoned and burned by shields, etc.
Now the question is, which sides shields? I would actually recommend that the negative attack creature go against its owners shield. Since antimatter is effectively taking control of a creature, that would make the most sense, and it would make shields a counter to the antimatter effect.