@kranu - I think 1000 variations of "Calibre Sync" applications being registered would trigger a few red flags, particularly since I would imagine they do not currently have very many users of their API. It is not in the spirit of the T&C to encourage users of this plugin to take such an approach. Were I at Goodreads I would be very tempted to just ban all of them in response, which would include the official account I have created for this plugin. Then we would be back to no-one being able to use it.
Also remember that it is entirely probable that if not already at least one member of the Goodreads team would come across this thread (a simple Google search would find it) and very quickly see what was going on.
As I posted on the "wanted" thread this plugin is all about encouraging users to maintain their data on Goodreads, not abandon it or one way scraping of data, so it is the sort of thing they should be encouraging. Right now I would rather just follow their recommended official approach and see where it leads us. They have said there will be some leniency and warnings first of which the low volume of users currently means it is not a problem yet.
Re your other problem - that looks like some sort of corruption of your Calibre/plugin install, it isn't a bug in the plugin itself. If you do a google for that error message you will see more information.