Fungus on the emulsion side will have eaten in and caused permanent damage. In my experience you can easily make things worse by trying to remove it. I normally clean the fungus from the non-emulsion side then dunk the transparency in carbon tetrachloride (for a minute at most) and allow to dry. As has been said, that does nothing to repair damage but should kill the fungus. This was the advice I was given many years ago by a friend at our local film archive. Apparently carbon tet can be nasty stuff, so leave a window open.
Cheers,
Steve