If you are making this soup for your consumption, I don't think you have to worry. When the soup boils, very little is going to survive that.

If you are making it for a large group of guests, then I would exercise caution. It's better to be safe than sorry when cooking for others. I know I've been in situations like this before, and that's always been my solution. I've never gotten sick from it, and nor has anyone else so far as I know.