While I'm not hugely qualified to talk about application of technique in a "rea" situation, I think that the amount of atemi that one uses in practice is one of the critically important decisions a teacher has to make.
I have seen classes (not Aikido, but I hear that it happens there too), where atemi is considered utterly indispensable for technique. These people will not practice a lock or throw without getting in at least one good punch first. From what I've seen, however, this results in an emphasis on speed and power, rather than precision of technique, to accomplish things.
While my guess is that these people would fare possibly better in a street fight after 1 year of training than a 1 year aikidoka, they miss a lot of the art in locking and throwing.
On the other end of the scale, I've seen Aikidoka who obviously know nothing about striking. They punch entirely with their arms, never drawing any power from their hip motion, and throw the top half of their bodies into it which does nothing but artificially unbalance them.
Sure, they throw pretty well, but I think that if one of their atemis ever connected, they would probably break/dislocate/strain something. That, and it leads to unrealistic attacks. Which is not to say that they're not committed in their attacks, or "insincere". They basically throw themselves. Other martial artists see these people and wonder if Aikido is anything more than a pretty dance.
So, back to the topic... I think that practice of atemi is critical. At the very least, Aikido needs to teach some striking to develop better ukes, but it also helps students become "real world" applicable sooner. However, atemi should be kept separate from the throwing/locking techniques (except those where it is neccessary for causing imbalance) to keep those techniques pure. If both things are practiced until they are "natural", the incorporation of striking into throwing as atemi should occur pretty easily.
Not that I have any opinions on the subject *grin*