No, I was actually talking about removing the serial connector alltogether. But if a serial connector doesn't use all it's pins and it would be possible to use two free pins of that one, I would consider that an option too.
As you may have noticed I don't know anything about electronics. So what I'm suggesting might not be feasible at all.

But I don't see why removing the pins from the docking connector would require me to terminate them ? If the player is in "home mode" and a serial cable is connected to the player, then those pins in the docking connector are also not terminated (I think), and it still works. Or am I completely wrong here?