I also have ssh keys setup, but with a passphrase (that is cached by the built-in ssh-agent). All admins have their own private key, the root accounts of the client machines have the public keys of all admins. I presume in your environment, that if you're root on one machine, you can login on all other machines w/o a password.
@adam:
step 2 - doubleclick the dmg
step 3 - copy the installer pkg to your client (in the terminal: scp -r /Volumes/munkitools-0.9.0.1789.0/munkitools-0.9.0.1789.0.mpkg root@somehost:/tmp
step 4 - install munkitools (in the terminal: ssh root@somehost installer -pkg /tmp/munkitools-0.9.0.1789.0.mpkg -target /
step 5 - configure client (in the terminal: ssh root@somehost defaults write /Library/Preferences/ManagedInstalls ClientIdentifier "test_munki_client"
As you can see, you can add a command after ssh that will be executed on the client.
HTH
-Arjen