I didn't know illness counted as disability, but ok. Even if everything you are saying is true, what does the law have to say about claiming disability after the fact? If the OP was indeed ill and "disabled" they should have addressed it with the teacher or dean during the semseter, not many weeks/months later.
It's great that you knew ahead of time and handled it appropriately, but if a student fails a class then shows up weeks later at the dean's office claiming that they were ill or whatever, it just doesn't seem right.
So often on SDN people are trying to get out of things that are a result of their own mistakes or shortcomings. For people who want to be doctors, very few take responsibility for their actions.
The syllabus almost always has something about attendance and attendance points. If you get sick at some point in the semester, it is your responsibility to handle it with the professor/dean or simply withdraw from the class. If all the information is made available to you (about illness and missed tests/class) and you choose not to speak up when you get sick, that is your fault.
This happened to me because I thought I could just write all the papers and show up for exams not realizing attendance was mandatory (this was my first semester of college). Did I go back at the end of the semester to cry to the dean that I didn't attend class or say anything about being sick because I didn't know better? Of course not. I took my "AF" and retook the class because it was my fault.
On the issue of illness and temporary disability, an illness becomes a temporary disability once it causes you to miss enough class that it begins to affect your grade. The vast majority of professors have "hold harmless" provisions that account for missing a day here and there for the common cold, flu, sinus infection, etc. You have to miss a threshold number of classes before they start docking attendance points, a pop quiz/in-class assignment gets dropped, etc. so that you aren't hosed if you're sick/absent for one of these assignments. I don't know what the precise threshold is in academia, but a reasonable guideline is two weeks. If the illness is severe enough that you will miss at least 2 weeks of class (or anywhere approaching that), I'd get the disability office involved.
I can't imagine it would be a big issue to claim the temporary disability after the fact, though it's undoubtedly easier to do it upfront. Students get ill all the time, and a lot of times they don't know that there are resources available to help them until waaaay after the fact. Like the OP, they may think that they are stuck with whatever the professor thinks is reasonable. At the same time, someone stuck dealing with an unexpected illness--especially one serious enough to cause extended absences from class--isn't really in a position to fight with a professor. Getting well takes precedence over arguing with a difficult professor, by necessity. A great example of such a situation is walking pneumonia. You get sick, miss a few days (maybe a week), get a little better, get sick again, get worse, and then get diagnosed after 2+ weeks of illness. After the diagnosis, you've probably got a few more days before you can realistically expect someone to get back in the saddle. In the beginning, the student thinks it's no big deal. In the end, the student may miss 2 weeks (low end) to 4 weeks (high end) of class.
The other benefit of going through the disability office is that they handle the medical documentation, doctor communication, etc. This way, only that one office has access to sensitive medical information. It prevents needlessly embarrassing the student needing assistance, and eliminates professors unfairly deciding what does and does not "count" as sick enough in their view.
All of that said, I have no idea what the OP's illness was, how long s/he was absent, and what the doctors dictated regarding lecture attendance. All of those things together would influence what the student disability office would suggest.
At the end of the day, I hope this knowledge will empower other SDNers should they find themselves in similar circumstances. When you're ill enough to cause you to miss enough class that it affects your grade, you're not stuck accepting whatever the professor dictates as a solution. You cannot be penalized for being so sick that you cannot come to class over an extended period of time.
To the OP (and anyone else), think about what "fair resolution" of this situation means for you. Do you want to be able to complete missed work (ie, exams)? Do you need alternative assignments in order to earn points that were available to other students, but which you can't really make up (ie, in class assignments, pop quizzes, etc.)? Be prepared with suggestions of creative ways to earn points that cannot be made up (presentation, paper, project, etc.). Would you be willing to accept an incomplete for the time being while all of this gets worked out?
Interface with your doctor as well. Don't hesitate to request additional clarification if it's needed. For me, it turned out to be a great experience. The doctors asked what I wanted them to request from the school, and the school gave me anything I wanted. It helped that I obviously wanted to be there, and that I wasn't asking for the sun, moon, and stars.
😉