Re: Bowing to Kamidana/Kamiza
If you are up for a little background reading, I would recommend Dave Lowry's book In the Dojo. It has a very detailed section on the layout of the dojo, the Shinto significance of the kamiza/kamidana and the associated rituals, and some Taoist ideas that also apply to dojo layout. Keep in mind that this is a Japanese cultural history treatise, and doesn't necessarily reflect how non-Japanese (and even some modern Japanese) view the subject.
I agree with what has already been said, especially about most dojo having tokonoma instead of kamidana. Each dojo sets its own spiritual and cultural tone in regards to both the kamiza ritual and aikido practice in general. Certainly if you have significant religious objections to the kamiza rei, then I would discuss it with your sensei. In the past I have met practitioners of different arts who as Jehovah's Witnesses were firmly against both the kamiza and shomen rei (and some even towards bowing to fellow students) just as they are against saluting the flag. As long as they remained respectful of those around them who did rei, the teachers, and the art itself, it generally didn't pose a problem once it was discussed with the sensei.
Personally, I view the kamiza rei simply as paying my respects to O-Sensei the same as I would if he were there, which doesn't interfere with my Christian beliefs at all. It is the attitude of the heart that constitutes worship, not the simple act of bowing, IMHO. I spend the short meditation time before training calming my mind and giving a small prayer for a safe, productive practice for all. Afterwards I do the same but instead express gratitude for my teachers and dojomates, and for the learning and growth I experienced in practice.
Best of luck in finding an answer that works for you!