Ennick,
It seems you're in a sticky situation. We once looked into exporting GA data for a client whose webmaster "accidentally" deleted 4+yrs of information. In looking to export all of the GA data and importing to a new one we weren't really successful, yet found this http://stackoverflow.com/questions/17891113/how-to-export-complete-google-analytics-historical-data which says unless scripting your own API to Google or using Next Analytics, you can do it, but are still limited to the data you can pull though depending on how much you need/they have.
To your question though, I'm not sure of the exact solution about unlinking the GWT and GA accounts as to what mess that could create. Interested to see what other Moz users have to say!
Hope this was somewhat helpful. -Patrick