Google allready knows this is an issue. This is why if you go to Google webmaster tools, you can choose to have a domain de-listed. If you remove one domain from the index, the other will get ranked and not be black-listed
There is one issue with this - the pages need to be temporarily a 404 ststus before google will remove the domain. Solotion - redirect (using DNS) the second domain into empty webspace while google delists the site
In google webmaster tools, go to the dashboard select the "URL Removals" then request the removal - google then put it on the list for removal
when the second domain is de-listed - repoint it at the first. Job done