You raise some good points and people should not shy away from them. Where I train the dojo trains us dually in Aikido and Atemi-Jujitsu. My suggestion is that you might find the history of the World Budo Kan interesting as the founder came to a similar conclusion that you have and developed Atemi-Jujitsu as a result. We still are trained and graded in Aikido because its considered the foundation of Atemi-Jujitsu.
In terms of Atemi Training that is placed with our Aikido we are trained in Western Boxing and Shotokan / Golden Dragon style Karate for the striking aspects.
I came to Aikido from a background in Krav Maga, Its my feeling that my current training offers me more options that Krav when it comes to taking someone down without hurting that person if that is my wish. I hate and eschew violence, yet recognize that in a self defense situation there are sometimes no other options than hard atemi striking to deal with it, yet as I train in Aikido I do see other options potentially opening up, yet like you say I agree that it takes many years of training to be able to do this effectively.
I guess there is plenty more I could say, yet it could be that our history on our website might get it across better than I ever could. - http://www.worldbudokan.org/