On GitHub you can restrict access to an organization's repositories from third-party applications. (Go to the organization page and pick "Third-party access" from the left-hand menu or just browse to https://github.com/organizations/<organization>/settings/oauth_application_policy.) When you do this, all previously issued SSH keys are blacklisted and Diffusion stops syncing with GitHub.
There is an error displayed on the page for the repository (ex: https://secure.phabricator.com/diffusion/P/edit) but I think it would be helpful to surface the error more prominently. Currently it's three clicks away from the home page to see repository errors.
This is the error text from GitHub:
>ERROR: Sorry, but @<organization> has blocked access to SSH keys created by some third-party applications. Your key was created before GitHub tracked keys created by applications, so we need your help.
>
>If you personally created this key, you can approve it at:
>
> https://github.com/settings/ssh/audit/<id>/policy
>
>Otherwise, please upload a new key:
>
> https://github.com/settings/ssh
>
>Fingerprint: 39:5a:5b:92:fc:b9:78:37:3c:f5:42:82:f2:90:5d:8c
>
>[EPOLICYKEYAGE]
>
>fatal: Could not read from remote repository.
>
>Please make sure you have the correct access rights
>and the repository exists.