There are Japanese people in Europe, some are even running for office, and Japan is not part of the European Union. There are Albanian people in the USA, some are even hosting reality TV shows, and Albania is not a US state (even if they are interested). Why shouldn't there be Orion people in the Federation, or Starfleet for that matter? That their world is not part of the Federation is not a reason at all.
What's more, I would like to believe that as much as the Federation stays further away from the internal affairs of its members than any planetary government, it still upholds certain standards, particularly regarding slavery. Picard's speeches in "A Measure of a Man" would seem to imply as much. I would assume that not only Orion women victims of slavery would find a home in the Federation, but they would be actively encouraged to do so, which would create a large Orion women diaspora on the Federation worlds.