Understanding that I have not actually used ColorJunki:
-- A printer is always going to have something manage color. Either an ICC profile at the application level, or the printer driver.
-- The warning is poorly worded. It means "Turn off the PRINTER color management and let Colorsync manage colors." Thus on the greyed out screen you will see that Colorsync is selected.
-- To use a printer profiler you normally print a target sheet. Your software should tell you what settings to use.
-- Next you read the target sheet and the profiler makes you an ICC profile of your printer/paper combination. (The same process that Canon, Epson, Red River, Illford, et al. follow.)
-- You can now use your new, ColorMunki created ICC profile to soft proof your image as you adjust it and, finally,
-- You use that same profile to print. (Remember, the profile is specific to a printer/paper combination and you will still have to set Quality/Media correctly for the paper.)
By selecting the correct ICC profile on the first print screen, you automatically kill printer color management and, with a bit of luck, a good profile, and clement atmospheric conditions, you will actually get a good print.
Trust me on this, I have been getting great prints from Aperture for years. My only gripe is that AP3 no longer lets me at the color options which I used to tweak for my cheap and cheerful Costco paper.