I think the bigger issues would be making sure your trainer doesn't touch your frame - that could damage the dropouts (or rear triangle).

and that you don't leave the tire clamped down to the trainer - that will deform the tire and make the wheel go out of round.

If you are spining is not a problem on the frame, I would not use my carbon bike on a trainer to similate hill climbing or any other type of high gear workouts. Your frame does not have any other option but to flex from the motion you are giving it, on the road you are not attach to anything and your bike moves side to side everytime to press on the pedals when you are climbing a hill or are on a big gear. So spin on that trainer and use your big gears out on the road. Good luck training this winter on that boring trainer :)

Latintriathlete

Can’t imagine that it is a problem – I do it all the time. Rode the first 60 miles of MOO on the CT this afternoon and to say the least, I was up on the cranks a fair amount. That said, I ride Ti, not carbon, and offer no opinion on the latter.
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Born again Heathen
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I think you are find getting out of the saddle; I'd just avoid really using the frame to throw around your weight the way a sprinter would.