I think it's fine to rule that the good multiclassed cleric/wizard cannot cast wizard spells with the [Evil] descriptor... as long as you also rule that the character can 'lose' any prepared wizard spell to cast a Cure spell of the same level or lower, that his prohibited schools as a specialist wizard apply to his cleric list, that the one additional spell of his speciality school per level each day can be prepared from either his wizard or his cleric list, and so on.
Either class features that affect 'spells' relate to the spells of that class, or they relate to the character. But when the language used is the same, it's inconsistent to say "This feature is specific, but this feature is global".