since an excess of this can result in an autoimmune disease
Not sure what you mean here.
The bacteria have a very good ability to not recognize "self" nucleic acids and incorporate them into the CRISPR Array. Though indeed the mechanism is not well understood. In fact one of the least well understood aspects of CRISPR relative to the bacterial immune system itself is the acquisition phase by Cas1 and Cas2.
Nevertheless, the focus of this blog was on the application of CRISPR editing in human B Cells. My initial description of CRISPR was just to get people on the same page, and make a joke about the use of one adaptive immune system to make modifications to another entirely separate adaptive immune system. :)