I see no reason why a sovereign Orion polity that meets the other requirements for Federation Membership could not join. If there's, say, an Orion Union and an Orion Republic, and the Orion Union governs its own solar system, is a liberal democracy, protects the natural rights of all its inhabitants, bans slavery and caste-based discrimination, etc., whilst the Orion Republic is a slave-based oligarchy? I see no reason why the Orion Union could not join the Federation while the Orion Republic stays out.
I suppose you're right. I was speaking more towards multiple states that share the same homeworld or system, like the Kes and Prytt in "Attached". Federation law clearly would not allow that. But in the example you just gave (when they control different worlds or systems altogether) I think it would be allowed.