Quick point of order: what I warned against was imbuing them with pseudo-religious importance. Of course these things have meaning. If they didn't have meaning they wouldn't still be around. I wasn't calling these things meaningless; I was suggesting they are not vitally important to the question of what is and is not aikido.
But is the "thinking steeped in religious thought" you're talking about really contained in what we wear and how many times we bow? And what's more, can't someone who has no knowledge of or interest in Buddhism, Daoism, Confucianism, and Shinto still practice real aikido?
Aikido is a product of a martial culture which is a subset of an educational tradition where a student's interest in or knowledge of what they are actually doing is of little importance. Students are like seeds, the instruction and practice are like water and sunlight, and etiquette, dojo cleaning rituals, training attire, and the like are the soil.