The way I would have implemented it, but would be keen to know how secure it is, is that you start with the md5 of the password (md5(password)). You then bcrypt or scrypt that md5 (bcrypt(md5(password))) and replace the md5 in your database with the bcrypt hash.
When a user logs in, all you need to do is to calculate the md5 first then check that md5 against the bcrypt hash you have stored.
I am not a crypto expert but intuitively it doesn't look like I would have weakened the security that way. You can't really attack bcrypt(md5(password)) much more than bcrypt(password). Can you?