1st- Most auto-immune diseases are not very well understood. To lump them all into one pile, for any cause, is doing the cause an injustice because it is an argument that can be explained away. There are thousands of auto-immune diseases, and their ratio of hereditary v/s non-hereditary is roughly the same as other types of diseases. We are just beginning to deeply understand the way tissue is recognized by our immune system. The pathology of this system is still decades away from being deeply understood.
I did an internship in college under a plastic surgeon who specialized more in breast reduction than in augmentation, although she did perform the surgery often. She mentioned (this was 7 years ago) that silicone was making a comeback and that it was banned more for bad press than for scientific reasons. She said that there was no scientific basis linking leaking silicone with any diseases. I am no expert on this myself, but she made a lot of sense. She had done silicone in the past and had switched solely to saline implants. The reason that many want silicone to make a comeback is because it feels more natural.
I haven't read much in regards to the scientific articles that caused the banishment of silicone. And personally, I could care less which filler is used in augmentation products. The only thing I do know, is that I have read a lot of incorrect material in these articles. I'd suggest taking them with a huge grain of salt.