If you are in a linux environment, epubs can be zipped from the command line or in bash:
zip -X0 "../$folder.epub" "mimetype"
zip -X9r "../$folder.epub" "META-INF"
zip -X9r "../$folder.epub" "OEBPS"
where $folder is a parameter in the bash script. Adjust the paths to your own folder structure. You first have to make the OEBPS folder with the html files (can be fetched from the internet using wget) and content.opf and toc.ncx, which can be created from the command line.
If you want to generate your own .ops and -ncx file you simply use something like this in your script:
"string to write to file" > content.opf
But if you're looking for a finished program to do it for you, I really have no idea. But it's possible to do it all from the command line or a bash script