If I am understanding your configuration, things are a bit more complicated. The equation you included is for a single interface. Your "arbitrary scatterer" probably has at least two interfaces. Even more complicated is if it does not completely fill the waveguide or has surfaces not perpendicular to the direction of the waveguide. Anyway, you can probably model whatever it is as just a slab of some thickness. You can search the internet for things like Fabry-Perot, or scattering from dielectric slabs. I put some information on this topic here:
**broken link removed**
See Lecture 1
Remember that a wave in a waveguide is not exactly like a plane wave in free space. So, the answer you get from a simple slab analysis may different slightly from your waveguide problem. Still, they should be reasonably close if the waveguide is single mode. If it is multimode, I don't think there is any closed form model you could use for an arbitrary scatterer.
Hope this helps!