I agree that this is a huge limitation (especially for groups like Students for Sensible Drug Policy who are trying to maintain contact with thousands of students on campuses across the country).
I think the solution is for FB to automatically include a footer with links in each message sent out through groups that allow folks to easily 1) remove themselves from the group or 2) stay in the group but unsubscribe from message notifications. This is how many orgs operate with e-mail blasts. Why can't FB implement a similarly simpe system with their messaging system?
We at Students for Sensible Drug Policy's national headquarters use Facebook all day long! Since we do student organizing (duh!) FB is a great way to stay in touch with our constituents. I even have a link to my Facebook profile in my e-mail signature block. I handle our congressional lobbying and media relations, and so I also try to connect on FB with Hill staffers and reporters I know; it's just one more way to keep building those relationships and move our campaigns forward.