I understand you are very devout in your Christian beliefs, however I personally feel you are expressing way too much concern in relation to religious conflicts with the practice of Aikido.
That said, let me explain. I've never, ever been to an Aikido dojo that performed any type of ceremony in any way remotely related to the "calling on our ancestors for strength". I've visited a dojo that performed a ceremonial class session to symbolize the beginning of a new year of training, however this was not quite the same as "praying to the ancestors".
Seeing "equality with the world" is something that I believe ties into the concept of harmony. I personally don't find myself any higher up the path of righteousness than an earthworm. My personal beliefs are such that I think all living things are equal. This may make me seem like an animal rights tree hugging hippie, but I'm not. I rationalize this belief by knowing that all living things have a certain purpose, whether it is using trees for paper or cow hides for clothing. These are by beliefs, and I don't impose them on any of my students; to do so would in my opinion be highly inappropriate. With that knowledge in hand, I would find it hard to find harmony in the world if I felt that I was better or more important than another living thing. At the same time though, I'm certain that believing otherwise would in no way affect my Aikido training.
I believe that if you follow the beliefs you have and maintain the type of relationship with God that is important to you, then all those around you will see it and understand your feelings and beliefs. I recommend visiting several dojo and finding one that fits well with what you want to accomplish.
Please understand that what I've written is in no way a challenge to your beliefs, I admire those who maintain a strong belief system and truly live their lives by it. I believe that doing so demonstrates a very strong character and willingness to succeed in all lifes adventures. Have a good day!