If someone wishes not to bow to the Kamiza in a dojo for religious beliefs then they should not nor should they ever feel compelled to. If the sensei has a problem with it go find another dojo. If another student has a problem with it, ignore them. It's that simple,
While I agree with this on the principle that one should not be forced to do something that they don't want do, I just can't really agree with this because of the value that I think it has in true martial arts. It is nothing more than a sign of respect, one of the pillars of MANY (if not all) of the martial arts. To me, it also shows a level of humility and humbleness, two other things that one should always have in the first place, but also that definitely need to be present in the martial arts.
Having an explanation of what it means, and what it signifies is showing that you are opening your mind, and are trying to learn the customs and origins of something (as the OP is doing); and I commend people for doing so when they don't know about something. And again (I sound like a broken record), an open mind is also something that is needed to learn, especially Aikido. I can not count the number of times I have read people saying to throw out your expectations of Aikido and just train.
To add a little context to my ideas, there was a Christian Aikido dojo in one of the little towns I used to live in, and they, with all their proverbs and things up on the walls, still bowed to show to their respect. A friend of mine trained at this dojo and asked the sensei why they did this (as he, himself was a fairly devout Christian). He told my friend (and of course I am paraphrasing here) that it was simply a sign of deep respect, and that god would take no offense to showing that kind of respect for other people. He also said that in accepting Aikido into your life, you were accepting another culture, and in doing so one should try to be as accommodating to it as possible, as it was not just a martial art, but a way of living life; one that was in tune with god's way.
Now, I am not a Christian, but this sensei's words really moved me. I never got to meet the guy, but I wish I had; I think we could have had some good discussions!