Bob, this setting is currently at the application-level and not the project-level. There's an open enhancement request to allow you to specify some connections as "sacred" which would mean that making changes against those connections would be MUCH more difficult. Things like deploy-on-save would not be available against those connections, and things like bulk deploy/delete, anonymous Apex execution, etc., would require explicit user confirmation. I'm planning to address that pretty soon in a metadata deployment/retrieval improvement-themed release. Until then if you're nervous about accidentally doing something to production, I'd recommend either not having that as a configured connection or perhaps "neutering" it by changing the username slightly to ensure that login fails until/unless you want to use that connection explicitly. That certainly falls under the category of "heinous workaround", but there's a real improvement in this area coming soon.
Regards,
Scott