Here's a possible workaround.
If you have an old Pages document that contains some proper typographical small caps, open it in Pages '09 under your current OS. Hopefully, you will find that the small caps still look OK. If so, copy at least one small cap character from this document and paste it into a new Pages '09 document. Then type your additional small caps just to the right of the pasted ones. (And then go back and delete the pasted ones.)
This works for me. I'm using Pages 4.1, which I brought it over to Mavericks (10.9.1). I had the same problem as you had with Pages 4.2 under Mountain Lion. Fortunately, I happened to have some old documents containing small caps that were created with Pages 4.1 under Snow Leopard (10.6.8), and I stumbled onto this clumsy workaround.
I might add that, once I've copied my small cap "starter" into a new document and added additional small caps text, I can change the font and/or size of the new small caps without losing their small caps attribute.
Perhaps this solution, or some variation of it, will work for you.