Hi there, As a 26 year old who was diagnosed at 13...primal teenage-highschool years. I know exactly what you're son is going through. Most people I've know with this illness, including myself have indeed missed school. Like it is almost impossible to function, or pay attention. Especially while suffering, that you nor the teachers, students could ever comprehend. With that being said my parents were harder on me, mostly my mother. I rarely missed school. If ever. However, I had great relationships with my teachers and they were understanding of my illness. They would let me go to the bathroom without asking...or sometimes I'd just have to leave and never come back. Honestly, it's so tough to try to go to school and deal with this illness. He most certainly isn't faking, but crohn's can be strange...I could be laughing one minute, then flaring in excruciating pain.
Now as an adult I still feel alone. I don't blame anyone, it's just no one can fully understand unless they are going through it.
I'd say just to have communication with your son, and his teachers. If he's sick he's sick, if he misses school he misses school. There are always lots of resources for education, he can always re-take classes or what have you. His health needs to be number one, and everyone in his life should be on board as support. If his school won't get on board maybe educate their ignorance.