Full disclosure: I hate this episode. I think its attempt to tug the heartstrings is trite and obvious, and the entire confict that drives it makes no sense.
That said, let's take a closer look at how its put together.
The main plot of this episode hinges on the age-old theme of Man versus God, or in this case Doctor Franklin versus a religion that won't let him save a child's life. The boy Shon has a blockage in his upper air passages, something that Doctor Franklin tells his parents is common in species with internal air bladders. This a clumsy "as you know, Bob" moment, given the parents presumably already know this being of the same species themselves, but does serve to make Franklin look condescending and Doctor-knows-best so I suppose it fits in the context of this episode - if not with his wider characterisation.
Unfortunately the mass in Shon's airways has hardened and requires surgery to remove. Shon's parents protest - "the Chosen of God may not be punctured" - and that's where this whole episode falls down for me. Setting aside that it's a swipe at real-world religions that don't allow medical interventions, and anyone's opinion of that, it makes no sense in the context of the religion in the episode. The parents explain that cutting open is only done to food animals, since they have no soul which can escape. People have souls, which can escape, so what's left after surgery is a soulless demon. There are hints at the reasoning behind it - late in the episode it's revealed their species is egg-bearing, they call themselves Children of the Egg, and Shon's father insults Franklin by referring to him as the descendant of "egg-sucking mammals". Clearly eggs are important: puncture the shell and you lose what's inside.
This doesn't work for me for a couple of reasons. The first is the reference to the Chosen of God in the very first scene. "Children of the Egg may not be punctured" would have set up the foundation of their beliefs right at the start. Instead it sets it up as being much like an Abrahamic religion (Judaism, Christianity, Islam), an effect only added to by Shon's father's insistence he read the "Parable of the Seventh Declination in the Scroll of Herrell" rather than watching the station's entertainment channels. It doesn't help that early in the episode Shon's father also refers to them as Children of Time. The egg stuff isn't introduced until comparatively late in the episode, by which point all it does is make a confused mess of their belief system.
The rest of this plot goes about how you'd expect. Franklin goes to Commander Sinclair to override the parents' rights; the parents go to all the ambassadors, not having one of their own, and ask them to intervene. G'Kar refuses because it doesn't benefit the Narn to help them, Londo because they can't afford it, Delenn because the Minbari are forbidden to interfere in matters of the souls of others, and Kosh for the reason given at the top of the post. It is a nice touch that their response to Delenn is an incredulous "You are refusing because of your beliefs?" Sinclair agrees to make a ruling, but it doesn't go the way Franklin expects. After speaking to Shon's parents, and Shon himself, and getting absolutely no help from Earth's government, he decides the neutrality of Babylon 5 must come first, and that this means the parents' beliefs must be respected. Anyone coming to this having watched the pilot will know this is the exact opposite decision to the one he makes there, in ordering the doctor to operate to save Kosh's life. Franklin mentions this and is told "it has to stop somewhere".
Of course, Franklin does the operation anyway. Shon's parents are mortified and violently reject him, leaving him sobbing and alone. Later they return. His mother tells Franklin they know he only did what he thought was best for their son, and that if they were allowed to forgive him they would. Now they will take Shon, and they have brought his lamuda, a travelling robe for great journeys. Franklin assumes they meant to take Shon home and lets them go.
It's only at this point Franklin bothers to find out any background to their religion, and discovers the lamuda is used for spiritual journeys. He goes after them, but Shon is already dead.
The B plot is barely memorable: Ivanova's going stir-crazy and persuades Sinclair to let her lead a squadron if fighters to rescue a stranded civilian transport. Following a scout, without back-up and against regulations, she discovers and neutralises an ambush and everyone is saved. It doesn't do much but reinforce Ivanova's hot-headedness, and add a counterpoint that sometimes if you go against the rules it does work out.
Having looked at it in more detail, I think my main problem with this episode is its heavy-handedness. The religion plot could have worked, had the egg-based beliefs been front-loaded instead of tacked on like an afterthought, and a little more care taken to distance it from existing religions. Instead it's a mess and the whole episode suffers for it. In that I suppose it serves as a useful lesson in worldbuilding, if nothing else.