I don't know of any definitive answer -- the opinions vary as much as the reasons for taking iodine. I found a thread from 11 months ago that discussed many of the points involved with candida and iodine. I know you've done tons and tons of research, and you may have already seen this, but I enjoyed re-reading it.
http://www.curezone.com/forums/am.asp?i=1509758
Thanks for finding that thread. I enjoyed seeing it again. I know what you mean about wanting to see research on this. From my subjective experience, I haven't had any sense that iodine was disturbing my good bacteria. In fact, one of the reasons I like Iodoral is that it's delivered more to my small bowel, and I thought that delivered a bigger punch to candida. However, iodine alone has not been enough for me, and Trapper's colloidal silver suggestion has been the one for me. It works great.