Sorry you both are having unnecessary stress at work. I think it helps to remember that all of us are broken, but some more so than others. Unfortunately there are more things than anyone would hope that are un-fixable. The choices are separation (quitting, etc..) or "dealing" with it (I'd more accurately term it "manage").
Pix, from what you describe it does sound like an HR thing. Not sure you can get fired for it, but attention should be brought up because at the very least it was unkind. Please keep in mind that in the end no one walks away unscathed from conflict. Life isn't fair.
Lemon, perspective changes everything. In the grand scheme of things your boss is low on the important things far below your health. AFAIK, by law, your doctor's opinion outweighs your boss'. <group hug>
