If you look at it through the lens of religion then the song's theme is that of a girl out of step with the religion of those all around her.
"Morning prayers took the girl unawares
She was late for class and she knew it"
Already shows she's out of step. She's 'late' compared to everyone else.
"The broadcaster had a voice that was soothing
She couldn't tell if it was a man or woman"
She's not really listening to the message, but daydreaming and wondering if it's a man or woman speaking.
"A patch of sun fell onto her (desk)
She put her head on her arms on her (neck)"
Assuming neck and desk are switched in the lyrics provided, the light's sitting right there on her desk and she's leaning back not paying attention to it (wondering where it is, maybe?)
The rest of the song just goes on repeating the same themes of religion being all around her but her being uninterested. The second stanza ends with and the chorus dictates the message of wishing she could be a part of everyone else's religion, even literally (by her daydreaming), thinking she'd be happy forever if she could just fit in.
The first lines of the next stanza more or less repeat the same theme ("Morning Has Broken" is apparently a hymn about a birth of the world, so her being bad at it indicates her own 'birth' isn't quite going off as it should).
But even so, she doesn't seem to be any good at the things everyone else is, like singing. So in this context, the line
"The choirmaster, usually a bastard, knows her mother's sick
He'll be nice to her"
Would mean that he can tell she's going through some issues ('her mother' either being her views or her faith) and deciding not to make it worse by yelling at her.
But at its heart and stripped of religion, the song's ultimately a lament about not being able to fit in with the rest of the world (in school or wherever), and the idea that everything would be okay if she could just fit in.
In this context she grapples with being uninterested in the things everyone else is interested in...the choirmaster (chorusmaster) and the line about her mother being sick might instead denote that it's understandable that she doesn't fit in (to the 'chorus') because she came from a bad background, wondering if she should "even be there at all." Therefore it could just as easily be a dig at the turbulence of adolescent existentialism.
There are a dozen interpretations for pretty much any of the lyrics in here, so it's really a bit of a blank slate. The religion aspect's a pretext, but ultimately irrelevant and a placeholder for similar situations of dissimilarity.
If you look at it through the lens of religion then the song's theme is that of a girl out of step with the religion of those all around her.
"Morning prayers took the girl unawares She was late for class and she knew it" Already shows she's out of step. She's 'late' compared to everyone else. "The broadcaster had a voice that was soothing She couldn't tell if it was a man or woman" She's not really listening to the message, but daydreaming and wondering if it's a man or woman speaking. "A patch of sun fell onto her (desk) She put her head on her arms on her (neck)" Assuming neck and desk are switched in the lyrics provided, the light's sitting right there on her desk and she's leaning back not paying attention to it (wondering where it is, maybe?) The rest of the song just goes on repeating the same themes of religion being all around her but her being uninterested. The second stanza ends with and the chorus dictates the message of wishing she could be a part of everyone else's religion, even literally (by her daydreaming), thinking she'd be happy forever if she could just fit in. The first lines of the next stanza more or less repeat the same theme ("Morning Has Broken" is apparently a hymn about a birth of the world, so her being bad at it indicates her own 'birth' isn't quite going off as it should). But even so, she doesn't seem to be any good at the things everyone else is, like singing. So in this context, the line "The choirmaster, usually a bastard, knows her mother's sick He'll be nice to her" Would mean that he can tell she's going through some issues ('her mother' either being her views or her faith) and deciding not to make it worse by yelling at her.
There are a dozen interpretations for pretty much any of the lyrics in here, so it's really a bit of a blank slate. The religion aspect's a pretext, but ultimately irrelevant and a placeholder for similar situations of dissimilarity.