Thats your best option, i have a similar dock and was thinking about making a little thing to sit into the ipod dock with the female adapter in the bottom, and having the charging and 3.5 sitting out the top.
That way i could just put my phone into it, upside down as i have the galaxy s it would work out well, also using a custom rom that supports a 180 degree rotation, so the screen would be the right way around aswell.
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