I'm not very familiar with gtkrc commands, but a quick web search shows several examples of what one could do. Or, you could get more extensive examples by looking at the source of a GTK theme file.
This stuff is pretty much beyond the scope of TKDO, but I could include some pointers in a FAQ or other documentation if you think it would help. And if things really need to be easier, I could probably find a way to let the user configure the font directly from within the GUI. But in most cases, I would think the desktop configuration tools (GNOME control center, etc) should be sufficient. TKDO will simply follow the desktop theme settings chosen by the user.
This is already possible by using GTK configuration.
For example, in my $HOME/.gtkrc-2.0, I have:
style "user-font" name="Verdana 9"
{
font_
}
widget_class "*" style "user-font"
This sets everything to the same font, but you could do more specific customization too.
Is this sufficient for your needs?