As a user, I'd like the dedupe tool to handle background activities required when merging contacts that have redundant Account Contact relationships. Cloudingo does this and Demand Tools claims to do this as well:
Resolution
Using the Dedupe module in DemandTools, accounts and contacts with redundant relationships can easily be merged without throwing errors and without having to manually remove any redundant relationships. DemandTools will automatically remove the redundant relationships so the records can be merged.
Merging Contacts with Multiple Account Relationships
When merging contacts with multiple account relationships, all account relationships will be moved to the master record. The account that is listed as the direct account on the master record will remain, and all other accounts will be indirectly related.
Merging Accounts with Shared Contacts
When merging accounts that have indirect relationships with a shared contact, the redundant relationship will be removed, and the accounts will be merged. The contacts are moved to the master record, and all direct and indirect relationships will remain intact.