The notion isn't as obscure as you might expect actually. First with the notion of gods being physical beings there are quite a few cultures that believe or even have evidence that their deities were at one point physical beings. For example in Gaelic folk lore the almost all of the deities tie in very closely with actual invasions of Ireland and are suspected to be based upon real individuals. Weather or not these individuals were actually divine beings is open to interpretation really although it's more commonly believed that whilst they were once based on real people they took on the divine attributes long after their death.
Although I've never used a crop circle as any part of a ritual and can't personally think of any specifically related examples there are one or two similar. To draw an example from Celtic lore once again the henges dotted across Britain are built in a rather ceremonial circular fashion (often related to various star constellations) that is not completely unrelated to your idea. Whilst I wouldn't say that the majority of crop circles have been created for magical means, or even that the first was, as we have strong evidence that the majority are merely pranks it is not inconceivable that a few practitioners could make use of them.
As for gods leaving behind crop circles in ancient times I personally find it unlikely however simply because they don't last long enough for them to be recorded. If you wanted to pursue the idea I'd recommend looking at more permanent structures typically built of stone, earth or even fossilized wood.