Are you sharing your library between MB and iTunes? Bonjour is what Apple/iTunes uses for sharing media libraries. MB didn't install it, iTunes did. As Steven said, MB doesn't need it, so if you're not using iTunes any longer, you can go ahead and uninstall it. I'd love to see a screenshot of the error.
FWIW, I've used every version of MB and I have iTunes installed -and- I have Bonjour installed. I have -never- gotten a message sure as you received.