Here are the rules:
Starvation and Thirst
Characters might find themselves without food or water and with no means to obtain them. In normal climates, Medium characters need at least a gallon of fluids and about a pound of decent food per day to avoid starvation. (Small characters need half as much.) In very hot climates, characters need two or three times as much water to avoid dehydration.
A character can go without water for 1 day plus a number of hours equal to his Constitution score. After this time, the character must make a Constitution check each hour (DC 10, +1 for each previous check) or take 1d6 points of nonlethal damage. Characters that take an amount of nonlethal damage equal to their total hit points begin to take lethal damage instead.
A character can go without food for 3 days, in growing discomfort. After this time, the character must make a Constitution check each day (DC 10, +1 for each previous check) or take 1d6 points of nonlethal damage. Characters that take an amount of nonlethal damage equal to their total hit points begin to take lethal damage instead.
Characters who have taken nonlethal damage from lack of food or water are fatigued. Nonlethal damage from thirst or starvation cannot be recovered until the character gets food or water, as needed—not even magic that restores hit points heals this damage.
Of course, it doesn't cover malnutrition. You would have to make house rules.
House Rules I would probably do
Use the non-lethal damage, but don't take it as damage. Since he is having some sort of food rather than no food, I would allow the non-lethal damage to accrue. After acquiring the amount of non-lethal damage that would normally result in lethal damage, I would instead give 1 point of Strength and Constitution damage. That will show that he isn't necessarily dying, but withering away. Normal food and rest intake would recover the damage as normal.
If you must use an illness
First off, malnutrition isn't really a disease, so I don't think cure disease would or should have any effect. If someone could cast Cure Disease on the target, there is no reason they couldn't cast Create Food & Water.
I would go with a dysentary, cholera or scurvy type of illness. Malnutrition would more than likely result in getting ill from other sources. There is a spell called Advanced Scurvy. You could model your natural occuring scurvy off of that disease.