As far as I know, they only affect your rakeback if you use them in one of two ways:
a. Using them on bonuses, which mrmonkey's site clearly shows.
b. Using them on FT Points, which is completely pointless, also shown on mrmonkey's site.
If you use your medals to purchase tokens to tournaments, you are not charged negatively from rakeback(just did this last month and can confirm.) Also if you purchase any of the apparel or accessories, you will not be charged negative rakeback.
To make things short, only buying bonuses and points(then spending them) will negatively affect your rakeback from IM Medals.