Paul, I'm so sorry to hear about the loss of your dog in the manner that it happened. That would be horrifying to come home to. I would imagine that it would be tough to reconcile your feelings towards the shepherd. There are just certain primal instincts that kick in in some dogs that transcends any training or domestication. I have had 2 dogs with extreme prey drive. No small animals were safe around them. And if they sensed any type of physical weakness (like seizures), then the drive really kicked in.
If you can somehow view your shepherd's drive as an instinct and not as a vicious intent, it might help you overcome the anger. I would have a very hard time with it as well. I would most definitely be keeping the shepherd separated from the chihuahua from now on when you're gone to avoid any possible future incidences. Take care
Mom to Millie, Roman, Snoopy & step sister to O'Boy