Enterprise Content Type Hub overwriting a Site Collection colum

We have a corruption issue caused by Content Type Hub Publishing (CTHP).

Scenario.

SP 2010 Server.

1. We have a site collection (MySiteCollection) created from a WSP.
2. The site collection contains a Site Column (SC) with an internal name of DocumentType.
3. The Type of the SC is Managed Metadata.
4. The SC is referenced by a SC level content type (MyContentType).
5. All was working fine. List items in document libraries present in sub-sites throughout the SC were correctly able to be tagged with the DocumentType column.
6. Then, a new CTHP was run. This had serious side-effects because present in the Content Type Hub site collection was a SC with an identical internal name ofDocumentType
7. The result was that now MySiteCollection had two site columns with an internal name of DocumentType and both of these columns had the same ID.The ID was not that of the original site column in MySiteCollection but rather the ID of the content type hub site collection field in (6) above.

Questions please

1. Should the CTHP work in this manner? Surely it cannot be correct that given the scenario above Microsoft will allow such a situation to occur? Shouldn't the default position be to log this issue andnot cause this problem?
2. To resolve the issue we propose to rename the field in the WSP that was used to createMySiteCollection so that the internal name is unique and therefore different to the field in the content type hub site collection. But when we used a tool to create a new site collection based upon this new WSP, and basically import the data from the original MySiteCollection into that new site collection, we end up with duplicate fields (albeit of the correct ID). There is no difference in the schema of these two fields. Is it safe to delete one of these duplicate fields?

Thanks for any advice and assistance.

Maz