I've only started looking through it, so I only have an inkling of how to manage this, but here's what I was thinking:
Keep track of how much SAN a PC lost on the occasion that she went nutso. Each month, the doctor makes a psychoanalysis check, DC=the remaining SAN damage+the patient's Cthulhu mythos skill ranks. If the doctor succeeds on the skill check, the patient gains back one point of SAN; for each five points by which he exceeds the DC, the patient gains back another point of SAN. The patient and other doctors may aid on the psychoanalysis check; the quality of the hospital may impose a modifier to the check from -4 to +4.
EX: Toby sees a little girl drinking a Pepsi; suddenly, she splits open, revealing a beautiful model inside. He takes 10 points of SAN damage and develops a severe phobia of zippers, in addition to gaining a rank of Cthulhu mythos ("that girl is EVIL!") He now has seven ranks in Cthulhu mythos. His friends cart him off to the Betty Fnord Clinic.
It's a great clinic, providing a +3 modifier to psychoanalysis checks. But his Dr., Dr. Lucky, is an absent-minded old fool constantly distracted by attempts on his life. The Dr. has a total modifier of only +2 to his psychoanalysis skill.
During his first month of treatment, Dr. Lucky makes a psychoanalysis check to cure Toby. The DC of the check is 17 (10 San points + 7 Cthulhu mythos). The clinic gives him a +3 to his check, and Toby wants to get better (and aids the doctor), so he gets another +2 to his check, giving him a total of +7. He rolls an 11 on his check -- barely enough to succeed. Toby gains back a point of SAN.
Next month, the DC drops to 16, and this time the doctor rolls a 19, getting a total of 26 on his check. Toby gains back 2 points of SAN.
Next month, the DC drops to 14. And so on.
It's a little more complicated, but not terribly so, and it's entirely in keeping with D20 rules, I think. How does that sound?
Daniel