During the 1800's using actual human bodies for training doctors in anatomy classes was illegal and against the current ethical and religious standards.
Medical schools hid that they were actually using human cadavers and the only way they could obtain them was through grave robbers who followed funerals to the cemetery to know where to dig.
However, they really didn't dig up an entire casket. What they did was dig a hole above the tombstone down to the coffin, broke off the end, and pulled the body out.
To transport the body to the medical school, they often placed it in barrels of whisky that would not only preserve the body but look like they were transporting alcohol.
After delivering the body, the grave robbers would then sell the whisky to the medical students, some of whom were actually engaged in grave robbing themselves....
So you can see that though this is really disgusting, it is etymologically possible that is where the term rot gut came from.
Of course another possible way the term came about is what whisky can do to your innards.
that's why i drink gin...
it only rots your brain.