This may be off topic, but I'm not sure.
The Tae Kwon Do or Shotokan nidan who looks at his yondan Aikido instructor and figures he'll be lost if he really unloads may be looking at things a bit skewed. If a Karate guy launches one of those amazingly fast tsuki's at a yondan Aikido person (I am assuming a certain level of competence here, we probably all know of exceptions), the Aikido person will probably be wondering how come he got hit. That said, I think that the Karate guy is assuming that because the Aikido person is a bit rattled and gets hit that Aikido by this person will not work, and that's probably not the case. The Aikido person will more likely realize that his canned technique will simply not work as it does in training and adjust to do more with body movement than technique. A Karate person, while incredibly fast with their hands and feet, will more times than not, be a bit static with their body movement. At the uppermost levels of both Aikido and Karate, I think that the movement differential is way lessened, but the Aikidoist has been practising since day one (I'd hope) to move his body off the line.
So the Aikido guy will be a bit overwhelmed by the speed and intensity of a good Karate attack, but I do think (assuming survival of the first attack) they will probably adjust.
More on topic, I very much doubt that most Aikidoists will have big success at utilizing atemi against quality Karate people if they are striking at ribs, arms, etcetera. I really believe the only likely atemi to have effect against such people is an attention getting flick towards the eyes, and don't hope for much success at leading someone who attacks with their back straight, their feet spread and their hips stable. Movement is the deal there. I think this may be a time where atemi is a smaller part of the equation; I don't make any claims at expertise, so please feel free to tell me if this observation is off base Mr. Ledyard.
This is only an opinion, and is open to adjustment.