Cooking beans with intact skins
According to this extensive bean cooking guide from University of Alaska Fairbanks, the secret is to simmer the beans gently.  Unfortunately, they have little more to say on the matter.

Kenji Lopez-Alt, in his column on Food Myths at Serious Eats says (emphasis added):


  Most of us have been told at some point in our culinary careers that
  salting beans will cause them to toughen. It's incredible that this
  little bit of culinary mis-wisdom still lingers, for it couldn't be
  further from the truth. A simple side-by-side test can prove to you
  conclusively that salting beans (both the water used to soak them in
  and the water used to cook them) actually tenderizes the skins.
  
  It's got to do with magnesium and calcium, two ions found in the bean
  skins that help keep the structure of the beans' skin intact. When you
  soak the beans in salt water, sodium ions end up replacing some of the
  magnesium and calcium, effectively softening the skins. Your beans
  come out creamier, better seasoned, and have a much smaller likelihood
  of exploding while cooking.


He provides this image of the contrast:



I believe the take away from this is:


Pre-soak your beans overnight, as your grandmother did using salted water
Cook them at bare simmer, stirring them minimally, to prevent physical damage to the skins.


The second can easily be achieved by placing the bean pot in a moderate (350 F, 180 C) oven rather than doing it stove top.