My (again amateur) understanding of O Sensei's ideas of being in harmony with nature is that of protecting nature, living in harmony with it rather than destroying it, and seeking to live in harmony with others around us.
...When I think about aikido and religion...Aikido makes it stronger, brighter, harmonious, deeper, whether you're Shinto, Christian, Buddhist, athiest/humanist, or whatever. Take from aikido that which makes your faith stronger and your life more enlightening and fulfilling, then smile and nod at the rest of it. I think that's what most of us do anyway.
That's very much in line with my own (amateur) understanding as well. The only possible conflict I can see is one of perception regarding the fundemental nature of existance: whether or not it's a duality or a singularity at its most fundemental level. As an agnostic, I'm not sure that's a knowable/applicable set of information, but the practical applications of harmonizing/joining/entering seem to apply pretty readily to an enormous range of relationships. It's that aspect which I think makes Aikido so universal. Like Sensei Ledyard said, it may make a difference later on down the road, but I think the bulk of one's Aikido training would probably be pretty useful.
As a side note, I know of several Christians who practice Shinto (not unlike your own Zen Christian description I imagine) and find it profoundly complimentary. In the same way I imagine a dualist can appreciate a Natural philosophy.