I've developed a technique where I mask almost all of the flash with my finger when I'm taking macro shots (so anything closer than 30-50cm). It does two things, first stops the flash wiping out and over-saturating the photo, and second stops the flash disturbing the snake too much.
Whether the flash actually disturbs any of our flock is debatable, once or twice Binky has recoiled as the flash has gone off, but that's probably as much down to the surprise.