First off you worded this perfectly and I understand exactly where your comming from. In the guild that I'm in we have had a lot of changes from Social, to Social Raids, Now to more Hardcore Raiding. We deffinetly have some old members that went the route of Top 100 guilds before we got more serious and they still have Alts that are in our guild because they like the atmosphere better with us.
What we do is 99% of the time we consider there chars Alts even thought the Main is not here. The only thing that would change that is the person can make at least our required raid amount per week which is 75% to be a raider. These "Alts" do not get first invites to raids but if in raid with us they do roll MS/OS with the rest of us as far as gear goes.
Granted these are still people that we like, if when the main left there was a bad taste in our mouth we booted there alts before they could log them in. lol