Hi!
I think you can turn it off by going to Preferences > Plugins and select "File Type Plugins".
Select the plugin "HTML to Zip" and disable it.
However...I'm not sure whatever ramifications, if any, this action causes. But I just tried it with my Calibre library and I imported a HTML file and it stayed a HTML file

The only thing it changed was the filename (to title_author.html) but it did put it in its own directory.
I hope that helps (a bit).
cheers
Edited: Oh, wait. You did all that. Sorry. Ignore me...