Did I mention B5 has many, many terrible guest stars?
Because it does. In fairness, many of them really don't have much to work with, especially bad guys.
JMS settled this argument back when the episode first aired. When asked, "Who's right, the Soul Hunter or the Minbari?" he replied,
The episode comes down hard against the Soul Hunters, though. There don't seem to be any non-Soul Hunters in favour of the practice (it is commented that the alien sector is in a panic over it), and even ignoring the psychotic principal Soul Hunter, Sinclair - who in moral issues tends to be JMS's voicepiece - bans Soul Hunters from the station.
One could defend the practice, and the episode isn't as strident as some Star Trek episodes (or indeed some B5 episodes) in setting up the other side as bad guys, but it's definitely picked a side.
^ As you say it depends on how you define a "soul". The simplest definition, (to steal a line from Star Trek) is "everything that is not of the body."
Even this is a very partisan definition. We're used to the idea that the soul is something incorporeal basically because efforts to nail down a corporeal essence were all failures, I believe there was a point the soul was located somewhere in the stomach in some cultures.
The soul, for all intents and purposes, is what distinguishes the living from the dead, in Latin anima, i.e. what animates us. So it's whatever makes us alive and, the assumption goes, is
us. The soul is a catch-all word for what makes me breathe and gives me the personality that assumes a Talaxian avatar is inherently funny.
You could pretty easily tell a sci-fi story about what this property is or what it's supposed to be (I'm not suggesting here there is
such a thing, only god and people who did science in school knows what biology is), but the specific word 'soul' probably has too overtly religious connotations - which was doubtless intentional on JMS's part.