With the standard groups and permission levels how do you stop "Site Members" modifying the Quick Launch or Top link bar?
This article references that users must have Full Control or Design permission to be able to modify the quick launch (for 2007, but afaik, this has been unchanged throughout the versions). It doesn't explicitly say which of the permission masks enables it. Has your Site Members group had it's permission level modified? Based on this, they should not be able to.
Looking over the permissions for design and contribute, Add and Customize Pages could be the culprit. Does your Member group have this mask included in their permission level?
Edit 1: And the corresponding top link bar article says the same thing, Full Control or Design permissions are needed to edit that.
To manage navigation for a site you must have at least the permissions obtained by being added to the default Designers SharePoint group for the site.