Keep in mind that under IDEA, if a child with a learning disability needs services beyond accommodations to continue to make progress, they should stay on the IEP even if they are now at grade level. The question is whether or not your son can continue to access the curriculum without the specialized instruciton, modifications or anything else on his IEP. It sounds like both you and his teachers don't think so.
As you've pointed out, the team should also keep in mind that once a child is in MS, the structure and supports in a general classroom tend to diminish, the amount of writing across all subject areas tends to increase. They should consider this when making the eligibility decision.
Finally, tell us more about your child's dysgraphia. Is it only a visual motor/handwriting issue or are there other issues going on? Often times organization, attention, processing speed, spelling, working memory issues create troubles in writing. Many of these were not tested based on the scores you posted. Here is a great article on writing evaluations.http://www.wrightslaw.com/info/test.written.lang.htm
If for any reason you are not happy with the results of the evaluation, you are entitled to an independent educational evaluation by a qualified evaluator of your choice paid for by the district. If you are not satisfied with how the meeting goes, I would recommend asking for the IEE, rejecting the finding of inelegibility. Until the new evaluation is completed, and the team reconvene's, the current (old) IEP stays in place under IDEA"s Stay Put clause.
As far as your initial question about dysgraphia impacting WISC scores - visual motor skills are required for the Processing Speed Index. Based on what you reported, they did not do these subtests. Occasionally motor skills can lower the block design scores a bit too, but your child seemed to do ok. The GAI basically takes out the negative impact of dysgraphia.
