I normally do intervals on the trainer around 90 RPM. Every 5 min I shift up, stand and pedal around 70RPM at the same power level. It helps break up the ride and keeps my butt from getting sore.

There are no issues with the trainer putting stress on the carbon frame. When I'm standing I'm not rocking the bike back and forth or leaning to one side or the other so I don't understand where any additional stress would come from.