First off: Would you let someone using the two-weapon combo or paired weapon gain defensive benefits from magic shield?
I can see your reasoning, and since we’re are dealing with none-too-realistic concepts like magic and stuff I can see a sort of rationality behind it, for balance issues and such. But I want to point out, for my own rationale, that a skill and style of martial arts, is somewhat different than magic, which performs its functions on its own, after being activated (at least in the case of the magic shield spell).
Whilst you say they would interfere with one another’s operation, and I can imagine this, I can also, as easily, imagine and see that the magical shield would in no way interfere with the "operation" of the shielding weapon style. The magical shield basically tries to stop objects, originating from an external source, from damaging the target of the spell. It is stated nowhere that this is anything but magical energy, thus its a logical observation (as far as logic can apply to magic) that this magical energy shield can be a "one-way" defence mechanism, hence it will not impede or interfere the caster, even if he/she is using two weapons. The protected character can, if you will, cut through his own magical shield to hit the guy in front him (I mean magic shield scaled up to wall shield would be something like that wouldn’t it? at least in my mind).
So, if using two weapons, and a combat style that focuses on defence (shielding weapon style, and perhaps blade barrier style?), makes magic shield useless, it follows that one should not be able to parry whilst using magic shield either, as this is the same function that both the spell and the shielding weapon style provides. No?