Currently there is no way to remove an App for Office add-in reference from Office 2016 (see below).
These add-in references are stored in the registry under a combination value that includes the add-in's ID GUID. This ID can be seen in both the add-in manifest and in the SharePoint Online application catalog (see below).
***Computer systems can be broken if registry edits are not performed properly, use this workaround at your own risk. There are no guarantees or warrantees of any kind **
There are a list of Item(1,2,3,etc) values under a key like this one:
HKEY_CURRENT_USER\SOFTWARE\Microsoft\Office\16.0\Excel\Web Extension User MRU\ADAL_z139970C84C528DEE9B3F50D634024065AABC863258DFEC9DB277DB4808974A9\File MRU
The entry looks like this value name = "Item1"
value = "[F00000000][T01D2B8497B0ABB70][O00000000]*51c8c010-87f6-4b2a-b105-e6128bc8b66z SPCatalog https://hempele3.sharepoint.com/sites/apps 220.127.116.11"
Since the add-in reference you want to remove could be anywhere in this list, it could be complicated to find and removed.
I have created a sample program that will remove these add-in references:
usage: RemoveAddinRef <app excel word powerpoint> <GUID of addin>
example: RemoveAddinRef excel 51c8c010-87f6-4b2a-b105-e6128bc8b66f
The GUID can be obtained from the "Apps for Office" catalog that can be found in the SharePoint admin tools for Office 365.
The .exe and Visual Studio source code is attached to this blog post. Project Download zip