Do I need to be concerned about a carbon frame if I attach a bike trailer?
I'm not sure of the type of bicycle you have, the trailer you're using, or how much you plan to tow. However, I have a BOB Yak that I tow behind a 2007 Specialized Allez Expert (with carbon fiber seat stays, but not chain stays), and I have not had any problems carrying groceries, textbooks, and other paraphernalia.

If your wife's bike has a similar setup (carbon seat stays but aluminum/steel elsewhere) it should be okay as long as you are careful about weighting the trailer and try to reduce the rotational forces (my trailer is single-wheeled, so it leans with the bike) by not standing in the saddle and rocking from side to side for hill climbs. 

You're also right about the wheel taking most of the acceleration and braking forces, as well as weight. On that note, you may want to consider how beefy her rear wheel is, if she has a lightly spoked rear-wheel, you may want to consider a heavier wheel to avoid destroying a 'lighter' racing tire.