Have you considered getting a full evaluation for autism for your son? Even if you don't think he has it, a full eval from specialists can be informative and may be what you need to stop the whole special ed process (or not).
Usually, you have a meeting to discuss eligibility for the IEP. Once it is determined that the kid is eligible, the IEP is drafted and implemented.
You keep mentioning how smart your kid is. Intelligence isn't always affected by autism (tho there are lots of low functioning autistic people). Autism is marked by impared social skills, speech/language delays and/or repetitive behaviors (to include lack of flexibility in things like schedules, and interests).
Call your Pedi and ask for recommendations where you can get a good evaluation. A full eval will usually be with a doc (medical, psych or neuro), speech doc, OT, and PT and will involve visits to school and home. Your insurance may pay for some of it and the ones I've seen use a sliding payment scale.
Your state probably has some advocates (usually volunteers) who know the special ed laws inside and out. My state has http://www.parentinformationcenter.org/
You could also contact them and ask questions about what happens with two parents disagree. I would bet that most of them deal with getting kids the services they need tho, so they may not be helpful.