Unfortunately this is a known issue, and not possible to overcome in todays version:
There are some group policies that control the Backstage area, but they are mostly all or nothing, removing all SharePoint referencing not just the Office 365 ones.
The workaround below should remove the O365 SharePoint on line content from the Office Save As screen and the "SharePoint" link in the contact card.
Current Status: This is a known issue, it could be addressed in a future version of Microsoft Office.
Posted by Warren_R_Msft in the blog Office 2013, Remove unwanted SharePoint Online / SkyDrive "Save As" backstage items November 26, 2013.
In Word there are options settings for Save available, but it's an all or nothing option on Show additional places for saving, even if sign-in may be required.
However, there is kind of a workaround posted by Johnny Zhang MSFT Support on the topic:
Based on my test, we can disable SharePoint site save location as below steps:
From Registry Editor, browse to:
Create a new DWORD value of UseOnlineContent, Set the value of UseOnlineContent to 1.
- Re-open Office application.
Reference: How do I globally disable SharePoint?
It's not a full solution to your problem, but it may give you hints in the right direction.