It's extremely rare for a guinea pig sow to injure a pup. Sometimes it will happen when an inexperienced mother accidentally bites the pup trying to get the sac off. My theory, and I have nothing to support this, is that it's more likely to happen when the pup is already dead (as in your case) and isn't moving around. With a live pup, it's moving in the sac while the mom is trying to get the sac off, so it's less likely to stay in one position and get badly injured. It might get nipped in a couple of places, but not in just one.
And like @Soecara, I think something was wrong with this pup from the beginning. I doubt that it was even born alive.
I think Joey is fine, so if she is pregnant, don't worry about her. The bigger likelihood is that there was something genetically wrong with the pup that could occur again, but you'll just have to wait and see.