Yes, basically. That isn't an unreasonable reading of patent law. If he had actually tried to apply Roundup to the crops or sell the seeds to other farmers, he probably would have lost the suit. As I understand it, he won because he wasn't actually using the patented technology, not because the patent was rendered void by the fact that the seeds were produced on his land.
The thing you have to realize about patents is that it doesn't matter if you yourself built the thing that implements the patent; what matters is just whether you're using the patented technology or not.
Which I find insane when it comes to crops. If the person had willfully taken some seeds and used them sure, but patent law really should have some sort of exemption for cases where the patented product is overtly trespassing. It's ridiculous that because some company patented a gene a farmer who never wanted the plant in the first place is limited in what he can do to his own property. (Can't use roundup, can't harvest his seeds, etc.)
It's a small step from this situation to creating a virus, patenting it and releasing it in the wild and calling all people that get the cold your property.
Patent ownership in this kind of case (the plants, not the people) needs to be dialed back.
Never mind a human virus. If Monsanto could create an airborn plant retrovirus they could potentially frame someone for stealing Monsanto seed and planting their entire farm.
The thing you have to realize about patents is that it doesn't matter if you yourself built the thing that implements the patent; what matters is just whether you're using the patented technology or not.