Leenia, perhaps I've heard different versions than you but the implication has always been murder to me.



The longest train I every saw,
Went down that Georgia line.
The engine passed at six o’clock
And the cab went by at nine.

   In the pines, in the pines where the sun never shines,
   And I shivered when the cold winds blow.

Little girl, little girl, don’t lie to me,
Tell me, where’d you stay last night?
I stayed in the pines where the sun never shines
And I shivered when the cold winds blow.

I asked my captain for the time of day,
He said he throwed his watch away.
It’s a long steel rail and a short cross ties,
I’m on my way back home.

The train run about a mile from town
And it knocked my fair girl down
Her hair was found in a driver’s wheel
And her body has never been found

(Lyrics typical to the versions I've heard copied from https://nativeground.com/pines-history-lyrics-tips-playing/)



The questioning of the "little girl" and then the highly suspicious circumstances of her murder, tied to the portending introduction of the train which murders the girl really makes me think it's about murder.

Of course, individual singers could adapt versions to be about sadness and loneliness, but most versions I've heard don't strike me that way.