Yes boiling stock does kill off bacteria that can be in the stock.
Boiling water, stock or anything else that may contain bacteria works to kill the bacteria that could be present in the stock or other thing you're boiling.
Most bacteria cannot survive the high and very hot temperatures of the boiling of the water or stock that is being boiled so they will die.
That's why when you're needing to drink water that may contain bacteria you are supposed to boil the water which in turn kills the bacteria.
Bacteria almost always die when they get to a boiling hot temperature.
So by boiling your stock it will kill off any potential bacteria that could be in the stock.