Re: How to reconcile?
Sounds like you may be facing the either/on monster. The way to reconcile is to accept and blend both. Being spiritually open and blending is not mutually exclusive from the martial protecting youself from a possible atemi. Thank your Uke for helping you remember both sides of the same coin we call Aikido.
IMHO, the exclusivsity of either/or is much easier (and more limting) than inclusivity of higher logic of both.
PS: Still writing? You certainly have a lot of god questions. The answers you find would make a great read. I think they are very typical of this journey. Write on.