The Phantom Does Not Kill... Unless it's a Last Resort
The Phantom is not The Punisher so he does not go around killing. Yes the Phantom has killed in the past when it is necessary and needed. Would suggest reading the Ethics and Moral for more information.
The decision to kill when necessary comes down to his ethics. Killing is an anathema to him, otherwise he could justify doing it (eg when the Python poisons himself, Phantom could have let him die (consequentialism) by taking no action, but instead he asks Guran to make the antidote (which he does for Kit), and a phantom gives the medicine to the Python (virtuous).
It’s dumb to do that, he risks letting an evil man live who he knows will kill again at the cost of himself who he knows will save the lives of others if he continues to live. This is not consequentialism.