Since MD5 hashes and bcrypt hashes are recognisably different: when the user next successfully logs in, check if they have an MD5 hash; if they do, use the password they just submitted (that you know is correct) to generate a bcrypt hash and then update your password database with that.

If you have a large number of inactive users, this might not be as effective (you'll still be left with lots of MD5 hashes in the event of a dump) but for other sites it can be quite useful.

You can also use the same strategy to increase the work rate of your bcrypt hashes in the future.