Unfortunately, I believe this is how it works. I'm guessing at this point, but I think the apps are sandboxed to not affect core functions of the TV. I'll forward your feedback, though, to the appropriate channels.
I have the Samsung UN55ES6100 LED TV, and have installed the Skype app. My question is about the "Sign me in when the TV powers on" option. With this option checked, I assumed it would load Skype in the background, allowing me to receive calls while watching TV. However, this is not the case. In order for me to receive calls, I first have to launch SmartHub. I then see a message that Skype has logged me in. From this point I exit SmartHub, start watching TV, and can now receive calls. It seems to me that I should not have to enter Smarthub first. That Skype should load, as the option indicates, when the TV powers on.
Did I miss something, or is this how it works?