The problem with your line of thinking is what we have with Monsanto. Farmer A plants Monsanto and through natural processes, his plants have their genes inserted into Farmer B's crops without his knowledge or consent. The wind, bees, whatever it took, was completely out of Farmer B's hands but the courts will make Farmer B either tear out every plant he has or pay Monsanto a hefty fee because their patented genes are now being 'used' by Farmer B. I don't know if its still the same way or if laws have changed since, but several years ago a man that worked for my father supplemented his income with around thirty acres that had to be wiped out because a court decided that Monsanto's rights were being infringed. He was able to appeal it, but his appeal wasn't heard until months after the sheriff's department forced him to uproot and destroy every plant. If he had been wealthy and called out an attorney on the spot, he might have prevented the destruction, but like most growers, he wasn't able to fight it until it was too late. While this guy was pissed off because that was his vacation money for the year, I wonder how many smaller farmers have been completely destroyed financially because of practices like that.
I agree that custom genes, if developed through some intelligent process and not merely 'discovered', should have the possibility to be patented. Trying to enforce that patent anywhere but inside a lab, (or after it is proved that the farmer fraudulently obtained the material), just feels unethical, though.