For the future, and without changing the way you work too much, it sounds as though you need to toggle Track changes so that it's not active when you add a footnote; not a major inconvenience if you use the keyboard shortcut. (ctrl+shift+E in 2010; can't remember what it is in 2007)

For what you've already done, you might need to consider a painstaking, one-off correction: turn Track changes off, accept each change – to clear the formatting of the footnote – and then turn Track changes on and reapply the change in the body text.

If you recognise all your changes, you could even use a character style to identify them: a) type in the new spellings; b) apply the style to the first occurrence; c) step through the document and use ctrl-Y to repeat the Apply style.

Hope you don't have to spend too much time unbolding the footnotes!