Respectfully, I don't think it's a good idea to thank the teacher for going against the IEP, if the OP intends to assert her son's disability-based rights. That would communicate, maybe, that her opinion is that the teacher's actions don't violate the IEP and her son's rights.
If this teacher hasn't for some reason realized that the OP's son has an IEP, or is intentionally violating the OP's son's rights, I wouldn't necessarily trust the principal or anyone else to recognize that fact and follow up by doing the right thing. And I think the relationship with the teacher is likely to be soured further in the short term, no matter what. So while there's a polite way of putting things, I'd do it clearly and a bit forcefully, to communicate the idea with no chance of misunderstanding, as well as the contextual message that the OP is not going to lie down on this.
If there weren't an IEP and disability mixed into this, I think it'd be almost a no-brainer to take the passive-aggressive approach to clue the administrators in on how the teacher is treating the entire class. Maybe a passive-aggressive zinger or two could be put in the message, a la:
We view organization as very important in our family. If my son weren't disabled, and didn't have his IEP which you must have overlooked, I could appreciate some theoretical training effect of punishing your disorganized students by denying them the chance to participate in the normal classroom experience. I'm sure it may be effective in forcing some students to either toe the mark, or else lose out on a lot of the fun of their educational experiences. There are just some students, like my son, who need accommodation because they're disabled in a manner that means that they just can't be trained that way without suffering harm. We need your help in finding a way for our son to learn and grow, without violating his equal right to education.
