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Aryeh Gregor:
According to http://dev.mysql.com/doc/refman/5.0/en/multiple-tablespaces.html, the process still basically involves shutting down the server so that the file is clean (no outstanding transactions).
As far as I know, this still won't work to move a table between two separate MySQL instances: "If you have a "clean" backup of an .ibd file, you can restore it to the MySQL installation from which it originated as follows".
Furthermore, the only way to do this consistently would be to stop replication at the same point on both servers, create the index on one, then copy it to the other. There is no advantage to doing it this way, since replication would have to be stopped on all servers for the duration of the index creation anyway.
- river.