Ok. The law about FMLA discrimination and retaliation use has it's limitations. While you can take the leave and your job is protected, that only means you are protected from retaliation for using FMLA. It doesn't mean that other forms of legitimate job elimination are not permitted.
This is why I asked about what reasons they have given, if any, for the job elimination. Clearly, you have the facts to support the initial framework of an FMLA retaliation claim. No doubt about that. The issue though will be what the employer gives as their basis for actually separating you. They obviously won't say "it was because he used FMLA" and if they did, great..the case is won. But they won't do that. They'll allege some reason, and if that reason is legitimate and non-discriminatory, then the FMLA claim won't work.
For example, if someone took FMLA and the employer already had in place a plan for a staff reduction (and the employee's name was on that list BEFORE FMLA was requested), then the employer would have a legitimate and non-discriminatory basis for termination. As another example, if the employee was already out on FMLA and the employer had a layoff, and included the FMLA employee, that too could be legal depending on how the employee was chosen. Is the employer a union employer, with "first in, first out" rules? Would the employee have been on that list, regardless of their FMLA use? Then that too is legal.
In your case, if the employer can point to any legitimate basis for your being selected for elimination, that has nothing to do with FMLA, then your FMLA use won't protect you here. Now, that being said, you've stated that there has been push back with your FMLA use. That's a good fact for you, and it calls into question any reason they would try to put forward as to why you were selected. You get to argument back too, to any reason they put forward, trying to show it as a pretext for discrimination.
I think it is worth your time to file a complaint with the Department of Labor, alleging FMLA discrimination. It would be better though to first make that complaint to the employer now, to HR if they have one, so that the employer cannot later claim that they never had a chance to cure.