Think I've got a fix, just running some local testing before sending it off to Jimm. There turned out to be a nice place to slip in special case "clean up source HTML" code into site-specific adapters.
I used
http://www.fimfiction.net/story/224372/ as my test case, it's much smaller and just has four emoticon images in the author's note - a lot easier to iterate on than the Godzilla story.

I noticed that converting it to MOBI and AZW3 did work even with the "broken" longdescs, it just took a little while for the converter to give up on them (it seems to be trying to access each URL sequentially, waiting for a while before declaring each a failure). For a story like that Godzilla one with so many embedded images that might have looked like it had hung permanently.