It would indeed create clone realms, where the governing body might be mostly in another realm (a realm ruled by "secondary characters"), damning the new characters there to a life without opportunity unless they are also active in the other. People who want to have both characters united will find a way.
I'm not saying every realm would be this way, however. And a variant of this 1 char/realm rule would probably be most appropriate if we were ever to fuse two continents together.
I really don't see how that could happen without a really well organized OOC clan. What you are describing would mean there would have to be a large number of people who feel this way, they all need to have a good field of influence politically
and they all need to be desparate enough to do this instead of going and experiencing a new realm.