Boiling soup is not bad unless you boil the soup too long which could overcook the soup and boil out and evaporate the liquid.
As long as you do not boil the soup too long then it's not a problem to boil the soup.
Boiling the soup can also kill some bacteria in the soup so that is a good thing.
Yes boiling soup does kill bacteria that may be in the soup.
When you bring the soup to a high boil temperature most bacteria cannot survive the boiling water temperatures.
However if you've left soup out overnight and it has actually gone bad then it should be thrown out even though boiling the soup kills most bacteria.
The soup could still make you sick if it actually has gone bad.
But if you think the soup has some bacteria in the soup then boiling will make the soup mostly safe to eat.
Some bacteria can survive boiling temperatures but for most bacteria the boiling temperatures can kill the bacteria.
Boiling temperatures are really high which makes it very hard for most bacteria to survive.