I don't know about causing eye damage, but my standard guidlines for using flash on animals:

-test with low power to see if they are afraid, or otherwise have an adverse reaction before moving up to 'game' power.
-don't use flash on an animal in the dark with dilated pupils. I make exceptions for skunks/raccoons raiding my bird feeder and they don't seem to care.
-when possible use diffused light. I find it easier on my eyes even when giving the same overall light levels (and it generally looks nicer too).
-I typically flash myself under the same conditions as I plan to put the animals through. Twice. If I'm not willing to do it again, it would be rude to do to anything else. I'll often use a higher power setting on myself as well, just to be sure I'm not too mean.
-always, animals come before pictures. Any sign of distress and I stop (flash or no).

That said, my gray treefrogs don't seem to give a toss when they are flashed. They don't seem to even register it. The flash durations are much shorter than anything animals encounter in nature, typically 1/10,000 of a second to 1/30,000 for my main flash, that I don't know they even notice (maybe lightning can compare?). This holds true for every bird I've ever flashed (mostly the ones at my feeder), chipmunks, skunks, 'coons, insects, frogs, snakes, etc., I've never met anything yet that's scared of the flash.


For pictures through glass with a flash, easiest way for acceptable results is to have the flash off the camera and positioned so as to not give reflections off the glass. This generally gives nicer light in any case, at least it gives you more control and flexibility over your lighting setup. A dslr with a hotshoe flash can work fine through glass if you are close enough to the glass (it will be far enough away from the lens axis to not give a reflection) or have a rubber lens hood that can be pressed right up against the glass to block reflections on the part the lens looks through.