Can pressure canning be replaced water bath canning?
No, it isn't safe, water bath canning is only safe for high-acid foods as the acid kills botulism. Low-acid food must be processed at 240F, 116C, and that can only be achieved in a pressure canner. 

When you pressure cook the soup it kills the bacteria, however when you then transfer it to the sterilized jars it could be contaminated on the way, and then the water bath won't be hot enough to kill the bacteria.