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