Flyboy340,
Yes I googled the Samsung auto-HDMI switching thing and there were lots of reports about it and some 'solutions' too in some cases, which varied from either getting a firmware update from Samsung, to one user who said he opened up his TV and removed a plug from one of the boards inside... I don’t recommend that latter course of action by the way!
I don’t 'believe' you will lose any audio quality with the connection to the optical port and it might turn out to be your only solution if there is no way to turn off the auto-switching of HDMI connections, but yes, you will lose the ability to do the voice control of TV, switching On/Off, muting the audio etc.
There is a way around this and that’s to add a Harmony Hub to your room... that device will not only switch your TV on/off, mute etc. It will also voice control the changing of the TV channels. I just checked your TV compatibility and it is showing as being fully supported by the Hub on the Logitech Harmony compatibility website.
Hope that helps.