Edit your existing ~/.gtkrc-2.0 file, or create one if it doesn't exist. This file will let you override parts of your selected GTK+ theme.
Add the following style
GtkTreeView::even_row_color = "#yourcolor"
widget "*NautilusNavigationWindow*" style "treeview-modified"
where "#yourcolor" is obviously the color you want; #F2F1F0 is the Ambiance / Radiance toolbar color that you may be looking to blend with. You can sample other colors using Agave, the GIMP color picker or any color picker tool.
Note that due to the side pane having a frame in all modes except "Information", it will not exactly blend in other modes the way it does in that mode; at least with the default themes. With some further hacking you may be able to work around the outline color and get it to blend exactly the same way if that's what you want.
You can find out more about theme styles in the GTK Theming Tutorial.