Using RSA directly as a block transform is extremely dangerous; the thing you have to remember about RSA is that, more than most other crypto operations, RSA is just a simple math problem. You are vanishingly unlikely to use RSA directly in your code without introducing a vulnerability.
That said, two responses:
(1) Yes, MD5+RSA is slower (and thus better) than just MD5.
(2) But we're quibbling, because bcrypt is tunably slower, designed specifically for this problem, free, and available for most dev environments.