The simple answer is to remove them from the database. But that requires a backup and down-time.
You could write a plugin (or use the script runner plugin, I think) to remove them with a bit of coding.
It's mostly harmless to do this, but it makes a bit of a nonesense of the history, because you can suddenly have issues with no record of their old workflow. It's rather odd to see records like "on Tuesday, it changed from Open to In-Progress", open up the workflow and find out the current one doesn't actually have Open or In-Progress. A spot of explaining to users is needed there...
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