That is really unfortunate and frustrating! I wouldn't say the door is closed just yet though. I agree with MON about asking how they will meet his needs next year. I am not sure if the grade acceleration would take the place of the subject acceleration or if he would need both. But if he only needed one, then grade acceleration would be so much easier for them.
I wonder if it would be helpful to talk with them and say that you are sorry that they have had a bad experience with the grade skip with another girl, but that this is a completely different situation and that it would be really sad if your son was not able to have his needs met because someone else had a bad experience. Every child is different and the IAS is supposed take each individual child into account and see if it is a good fit. Maybe they could do a trial thing and see. What if they put him in with some of these peers for part of the day now to see how he would do. Nothing actually set, but just visiting and working with the classroom some.
Anyhow, you sound like a great advocate for your son! Keep up the great work, it is definitely a challenge some days...or most days rather. : )