Okay I'm gonna go waayyyy out on a limb here, and hopefully won't have to practice any virtual ukemi. My knowledge of Gnostic beliefs stems more from the amateur study of early Christian history and the alternative religious texts and sects floating around at that time, and as such is very rudimentary.
That said, please allow me to quote from the 32 Fold Confession of the Order of Nazorean Essenes.
I. If, O Great Life, we have sinned in any way against the five kinds of living beings: the two-legged, four-legged, those that fly, those in the waters, or those that crawl on their bellies -- if we should have hurt or frightened them, stolen or used their milk, eggs, or body parts in any manner, participated in the preparing, serving or eating of their flesh or oozings, or benefited directly or indirectly from their death or torture - then we now, O Great Life, pray to be forgiven.
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. If one honors nature and living things the way the above confession indicates, I don't see how that is in conflict with O Sensei's teachings on harmony with nature, except that to my knowledge he did not go to that extreme. One of the 32 Commandments of the Order forbids contamination, including the contamination of the environment. Again, I see that as perfectly in line with what O Sensei taught and what others after him have also said. I do have to ask in sheer ignorance and honest curiosity, however - if nature is so evil and the natural world was created by dark forces deserving of no reverence, then why do you seem to have laws and confessions that seem to hold the earth and all of its life in such high regard?
When I think about aikido and religion (especially in regards to my own odd little Zen Christian thoughts), oddly enough a commercial comes to mind. Do you remember a few years ago when BASF was running a series of commercials to build their brand identity and awareness? They'd say things like "We don't make the snowboard, we make it faster," "we don't make the paint, we make it brighter," etc. That's how I look at aikido. Aikido does not make the 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.