Were you ultimately allowed the FMLA leave that you requested? Aside from the company giving you the run around on your complaints, the conflicting assignments, and the write ups for alleged performance issues have you suffered any other problems from the employer after you requested the FMLA leave? In particular, have you suffered any problems that cost you money or status, like reduction in pay, demotion, reduction in hours, etc?
I'll note a couple of things here that really do not come into play with a retaliation claim. First, the company has no obligation to fire your supervisor, suspend him, reassign him, or take any other disciplinary action action him as a result of your allegations, even if the allegations are found by the company to be credible. The company's obligation here is to make sure that the retaliation and discrimination cease. If the company can do that with simply talking to the supervisor then it has solved that problem. Second, the employer does not have to handle the investigation of the other employee's complaint against you in any particular way. Indeed, the company doesn't have to investigate it at all if it doesn't want to. What will matter is that the employer does not illegally discriminate against you as result of the complaint. For example, if the company treats you worse in this situation than it would another employee in the same situation and the reason for the different treatment is your race, color, national origin, sex, religion, etc then that is of course illegal.
It looks like the company may be set to terminate you. If that termination is because of the other employee's complaint or because of performance issues then there isn't any recourse for that. If the termination is because of you exercising your rights under the FMLA or because of your disability that would be illegal and give you a wrongful discharge claim. The problem is proving that the reason for the termination was illegal. That is often hard to do absent some "smoking gun" evidence like a statement from the employer stating that was reason or being able to show some kind of pattern of illegal retaliation or discrimination by the employer.
However, I don't know all the details of your situation and what evidence you have to support it. If you get terminated you ought to at least consult one, and perhaps several, attorneys who litigate wrongful discharge claims to see if you have something worth pursuing. Most will give you a free initial consultation. So you have nothing to lose by talking with a few of them. Note that you do not want to wait too long, you have at most 300 days from the discriminating event to file a complaint with the EEOC for a claim of illegal discrimination and you must file a timely complaint with the EEOC before you may sue the employer under federal for illegal discrimination.

