Hi,
When I read the Original Post the first time I did not spot the ID for a Facebook Chat ID.
They have shut done their Jabber server and are using a more proprietary chat method in the normal Facebook pages (no Second ID)
It does mean it will not work in Messages anyway which may be why you want to delete it.
The similarity I had was my Google Account is also through a Jabber server and I could not get it to login to make any changes.
The System Preferences > Internet accounts seems to cause the creation of the com.apple.account.service.auth or oauth token item.
As I said I deleted this and I happened to find an out of date Certificate that I also deleted.
I was then fully able to "turn Off" the Messages option in the System Preferences > Internet accounts pane for the Google ID (in my case).
Following that the Minus item worked in Messages so I could delete it.
Then I re-added it in my case I wanted it to work.
Try it this way:-
In the Keychain leave anything that is just the Facebook Application Password that might be used in Mail and or Messages.
Delete Anything that relates to the com.apple.account.Facebook.auth (or oauth) tokens There are likely to be Refresh ones, Expiry date ones and nosync ones amongst others.
Check there are no out dated Certificates.
Now go to ~/Library/Preferences and find the com.apple.iChat.Jabber.plist item and drag that to the Trash.
(Hold the ALT key down whilst using the Finder > Go Menu and then choose Library that appears in the menu followed by navigating to Preferences)
Make sure the Messages option is turned Off in Internet Accounts > Facebook.
Hopefully the Account should now be deletable in Messages (Active Minus button.)
7:56 pm Sunday; January 3, 2016
iMac 2.5Ghz i5 2011 (Mavericks 10.9)
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