I have used my carbon bike on the trainer but I built up my old Cannondale for the trainer. That way I don't have to keep taking it off and on.

However, for my rehab from ACL surgery, my LBS set my carbon bike up for the trainer. Because I don't have full range of motion in my knee they raised my saddle and handlebars. I'm even using my American Classic wheelset.

Anyway, my LBS voluntary set the bike up for the trainer. If there had been a concern I'm sure they would have recommended against it.