no everything will be written over with this guide no need to uninstall anything. You can go from chapter 2 and update HB at a later date if you want- When you do this though you will need to install ios58. As the newer HB runs through ios58. A bootmii backup is advised to.
EDIT: I'll just change this post completely. Thank you very much for all the help narse1979! My Wii is now running my game backups as it was, and it feels good knowing my Wii is properly updated, and knowing I can check what IOS' on my system. Learned a lot about Wii hacking today! :D