If the Aikidoka here do not mind, I would like to contribute in a small way?
1. For the original poster, have you actually sat in on an adult class in both dojos and seen something that you like? And, as in Aikido, have you crossed hands with the sensei/sempai to discern the quality of teaching? Those two things matter the most, more than lineage, or style.
2. As a Goju stylist with a strong interest in Aikido and CMA, I think that there is much to these arts that complement each other. Personally, while you want to get something that doesn't interfere with your Aikido, it sounds like you want to 'fill in the holes'. To learn to kick and punch just takes time and practice - time away from Aikido. I personally wouldn't join a dojo for those singular reasons.
3. Why bother with any art that is going to hinder your base art? Meaning, any art that focuses on low-stances, not-moving, not-blending, and filled with too many katas/time wasters? What I read about the karate school you're looking at doesn't bode well. For a long-term committment, I'd consider a karate style that will lend insight into your base art. Of course, being biased, I'd suggest a sound Goju school.