Without more details its very difficult to provide any specific help. Normally the best course of action is to request disclosure and see what the evidence against your wife is. With two charges, its quite likely if you meet with the Crown theyll drop one in exchange for a guilty plea on the other. Just read through the forums and youll get some good general advice.
In regards to the red light charge, one important consideration is if your wife was already in the intersection or not when the light turned red. If she had already entered the intersection and was waiting to turn when the light turned red, the charge is incorrect. Its only illegal to enter the intersection on a red light, not to finish your turn if youre already in the intersection.
In regards to the second charge, Im not sure I understand why your wife was charged. If she had a valid ownership (meaning stickers on the plate and back of the permit), she shouldnt have been charged.