Just saying, if an org has it's members list set to secret, I'm really going to take a closer look.
The best way to have a secret organization is to:
- Not create an org. Just have a secret chat channel and an informal structure. You need to trust everyone for this to work.
- Operate through one or more front companies. Don't name your group "Black Mesa Mercs, Inc.", name it "Timmy's leet miniNg group12". No one will look twice at that. Better yet, have a bunch of orgs like that, each controlling a small section of your "real" org.
- Infiltrate existing organizations and make them work for you.
Now, when it comes to orgs you don't want to be affiliated with, there are a different set of options. But, general rule of thumb: If you don't want to be affiliated with a group, you shouldn't join that group. When you join a group, you join their culture and their wars. You get their reputation, enemies, and friends. If you aren't okay with that then you really should not be joining.
There are some legitimate reasons to not be affiliated with a group. Perhaps you are member of a "pirate" group who has a trader/hauler alt character for doing non-combat things, while you are a proud member with your main you don't want people shooting at your alt all the time. In such cases, your group could create a cover group for your alts. Name it something like "Teran Unions" and people won't realize the affiliation. Or, perhaps, you want to covertly support a group (maybe in a war), in which case do things informally, working with the group without actually formally joining.