I'm trying to get Amarok to play a specific song from the playlist. However when I use the --queue option it adds the song to the playlist a second time, after doing this a few times its easy to see my carefully organized playlist turning into a mess. Is there any way to trigger a specific file from the command line without disturbing my existing playlist?

Which exact Amarok version are you talking about?

I'm on... 2.3.1

There has been some work since 2.3.1 on the queue function and a new version will be released in the upcoming Amarok 2.4.
You can already test it with Amarok 2.4 beta: http://amarok.kde.org/en/releases/2.4/beta/1

In the mean time, normally selecting a track in the playlist and right click to queue it should not add it again, I can't recall a bug report doing that.