It turns out you can have separate GTK rc files for separate apps, just by setting an environment variable. For this example I'm using this theme: https://github.com/axxapy/Adwaita-dark-gtk2
First, clone the GTK theme you want into a directory such as ~/.config/geany/gtk
mkdir ~/.config/geany/gtk2/
cd ~/.config/geany/gtk2/
git clone git@github.com:axxapy/Adwaita-dark-gtk2.git
That's it. You only have to do that part once. Now any time you run geany, just set an environment variable first, like so: