My youngest son and I had MRSA - and it's pretty darn miserable BUT we were able to keep my husband and other two boys from contracting the infection. Our pediatrician gave us a prescription to swab into the nostrils of the two boys who did NOT have MRSA. I sterilized all toys and hard surfaces. I made sure to keep our wounds covered and carefully cleaned. I went a little nuts with hand sanitizer and Lysol spray.
The biggest thing involves open wounds. My son and I both contracted MRSA through existing wounds. Your nephew is being treated very aggressively - and by the time you go into labor will almost certainly not be contagious. If your children don't have any open wounds AND your sister has cleaned and disinfected her home careful, there shouldn't be much of a risk . . . but I would err on the side of caution and request the prescription for the nasal swab medicine.
It's my understanding that my son and I will carry MRSA in our systems forever. It's definitely NOT the worst thing in the world. Early and aggressive recognition and treatment is the key because MRSA is a staph infection that is resistant to the "normal" antibiotics. I recognized the problem immediately and my eighteen month old and I were treated successfully with oral antibiotics. We didn't need shots or IV treatment. But this HAS changed how I take care of even the tiniest boo boos and it has DEFINITELY caused me to increase the disinfecting I do around the house because I don't want my other boys getting this!