You may be better off with two versions of the story rather than an alternate chapter.
That's what I'd do. I often provide a clean version, which I post to finestories, and an adult version which I post to SOL, outlining the differences on my blog so readers can choose between the two (though, honestly, most readers are unlikely to see the blog entry since they only read a story once it completes).
However, if you decide to post both version on SOL, I'd change the title and post it as a separate story entirely, with a line in the story description about the 'softer version of the story' for those intrigued by the description, but turned off by the codes.
The story is currently 16 chapters, with the one chapter being the only one that concerns me.
Ahh, that's an entirely different problem. In that case, I'd post a warning at the start of the problematic chapter, warning sensitive readers in case they want to skip it entirely, or at least skim it to get the basics without being squicked into quitting the rest of the story. You'll have to decide whether posting two separate stories is a better option than posting a warning on a single chapter.
As for posting the same story twice with just the one chapter difference, I doubt if readers would want to go through the same chapters in both just to get the one that is different.
In my option, readers would choose to read either one story or the other, rather than each reading both. After all, if someone reads the explicit version, why would they want to read the clean one? Likewise, if they enjoy the clean version, why would they want their experience destroyed by reading the squicked version? Instead, let the readers decide for themselves which they'd rather read.
As a reader who hasn't had the problem I would feel happy to have a conventional link in Chapter 15 to and to see Chapter 16A with a bold or italic header stating that Chapter 16B is the original but may be too [violent] for some readers and giving a link to Chapter B for those who want that version At the end of both versions have links to Chapter 17 and also to the other version of Chapter 16.
Of course I'm not sure if this is technically feasible.
That would be easily to implement, though you'd have to post the links after the story posted. Just get the page address for each chapter, and then attach an < a href="">name of chapter< /a> html command.