Yes and you can also boot OS 3.9 from the CF card if you wish.
IIRC, you just have to rename your CF card to AmigaOS3.9, AmigaOS 3.9 or Amiga OS3.9. It's 'one' of those, but I believe it's the first one. May also have to open a shell and type an assign too in order for the automatic installation to repeatedly call upon 3.9 during installation.
If all of the above fail for you, simply copy the necessary files from the CD to the CF card and then onto your Miggy.