Hi Julie. Since you used the word "legal" twice, I feel the need to preface my response with the disclosure that this site does not provide legal advice, and I do not personally give legal advice on this site.
Having said that... I would start with telling the school (in a nice way) that while you understand that they are working on this gap, that it not a viable reason under the IDEA for not providing specialized instruction for which your son qualifies. If the IEP team has decided that Directed classes are needed for ALL of your son's courses, they shouldn't be able to pick and choose in which classes they are provided. An exception might be if your son was only showing low scores/data/grades in math and ELA and didn't show a need in Social Studies and Science. But that doesn't seem to be the case here. If it were, you would need to show the data (standardized tests, grades - they're not really data, but if he's getting C's and D's in Social Studies and Science and A's and B's in math and ELA, it would be relevant) that he is falling behind due to not receiving the specialized instruction that he needs. Also, it makes no sense if the need is related to his disability and ability to learn and NOT his inability to learn in a specific class(es). The fact that they've already discusses him being in Directed classes in all academic courses in high school is additional proof that the team feels he needs this in all classes. Finally, if you feel you don't have enough data, ask for an IEE with observation in class, that will hopefully come back showing he is unable to keep up in the gen ed classroom setting.
If the school district already agrees he needs Directed classes for Social Studies and Science but say they "can't" provide it, they need to think outside the box. "Can't" is unacceptable if the need is there. They could hire another special education teacher - even just part-time if that would be enough. They could assign (and hire, if needed) a 1:1 para. At a minimum, they need to be providing him with pre-teaching and post-teaching of the curriculum in these two classes to help him keep up. If what they try doesn't work, then they need to try something else.