Hi Jo,
I'm not sure it is App Nap that's causing the problems. Looking at the documentation it seems like it shouldn't be slowing TG down. However it's definitely worth turning it off for TG and I will checked whether to see App Nap is having an effect.
I did a render test with App Nap turned off for TG and OS X 10.9 rendered a bit faster than OS X 10.8. I only did one run though, normally I would do three and average them. In any case, I don't think Mavericks is any slower to render aside from any potential App Nap issues.
Regards,
Jo