Here is a workaround that can be enacted purely using non-root config:

1. Add the line "unset SSH_AUTH_SOCK" to ~/.xsessionrc (creating it if it 
doesn't exist).
2. Run gnome-session-properties and untick "GNOME Keyring Daemon Wrapper".

The first makes /etc/X11/Xsession.d/90x11-common_ssh-agent not decide
that it should not start since there is already an existing agent. The
second stops the g-k-r envvars being reinjected into the X session at a
later point in startup.

-- 
Unable to disable the ssh module of gnome-keyring
https://bugs.launchpad.net/bugs/275010
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