Personally I print everything on the printer, not on the keyboard.
The Macintosh Biblioblog has a Special Key Symbols reference page that details the Unicode for various characters, including the command key (⌘). At the bottom of the page there is a link to another article that describes how to enter Unicode.
I hope there's an easier way.
GoSquared also have a Reference for EVERY Character Key on a Mac. Unfortunately this does not seem to include the command key. However it does have an easy keystroke for the older command key symbol (): Option-Shift-K. I wonder if a work-around might be to use that keystroke in your document, then do a global search-and-replace changing all occurrences of to ⌘.