Interesting hypothesis, and one that I was considering about 9 months ago, when Jon was having diarrhea daily, and all sorts of seizure daily.
It seemed that both the diarrhea and the seizures cleared up simultaneously, but we were treating both simultaneously, so hard to say if one helped the other, although I'm convinced that's the case.
Jon trialed Lamictal several years ago, and had a strong allergic reaction. However, the drug that's currently working for him is Zonegran, along with the Ketogenic diet. He's been seizure free now for 6 months, and also been having normal bowel movements, with just occasional and brief flare-ups of his Inflammatory Bowel Disease during that same time.
His nutritionist/pediatrician (we found one who was both) put him on a regime of a high dose of zinc (followed by a lower maintenance dose), pancreatic enzymes (he continues on these), and probiotics (only when having a flare-up) and we temporarily adjusted his diet to take out foods that might be triggering problems (most of which have now been added back in). The zinc seemed to help more than anything else.
His neurologist increased his dose of Zonegran, took him off the other seizure meds, and we tweaked the ketogenic diet he was already on -- for one thing -- adding in MCT oil, which has great benefit for those with malabsorbtion issues.
Malabsorbtion seemed to play a big factor -- if Jon wasn't absorbing fats properly, this would skew the ketogenic diet. He probably also wasn't absorbing his meds properly.
But, I don't think malabsorbtion was the only issue. I suspect that there's some underlying autoimmune disease that is causing both his epilepsy and his IBD.