I use the better beamer with a Right Stuff flash bracket, which raises it off my 600 about 6 inches, but it doesn't do much in avoiding red-eye. Unfortunately (for taking pictures) the darker it gets, the wider the eye diaphragm of the animal, so it makes it worse as compared to daylight shots. I'll go with a slower shutter speed, higher iso, even mirror lockup, and remote cord (assuming that's possible) before I attach a flash. I took lots of shots this spring of great horned owls, and got some vivid "birds from ####" with the flash. Nocturnal animals usually have larger eyes, which exacerbates the problem.
I have resorted to using PS in making corrections, and there are various ways of doing it. Arthur Morris has a workflow guide out, I think it's $20, and it explains how he deals with the correction through PS. You might check out his site, which is
www.birdsasart.com Attach is one of my owl photos corrected through PS.
http://imagenorthwest.com/owlgh14-05.jpg