What can be done to address permanent sutures on patients with autoimmune issues?

I doubt those permanent sutures will have any effect on your autoimmune issues. If they become painful or swollen they are easy to remove

It is indeed possible to remove the sutures used for the suspension of the deep plane facelift, but this would generally require reopening the scars unless the issue is limited to a single point of irritation near the skin’s surface. In such cases, it may be possible to address it directly without leaving significant marks.

At six months following surgery, the stability of the deep plane facelift may remain intact, even if no additional dissolvable sutures are placed to support it. This is particularly true if the cosmetic outcome of your surgery has been good. It would be worthwhile to raise this concern with your surgeon to determine the best approach.

It is also essential to assess whether the problem is due to genuine inflammation in the tissues or primarily a mechanical irritation caused by a suture knot. A thorough evaluation will help guide the next steps.

Autoimmune diseases do not preclude the use of permanent sutures. It's unfortunate that your surgeon became irritated instead of understanding your fears and explaining calmly. Any perceived inflammation you might have is not from permanent sutures.