Then he acted in a way that made it clear he was using the patented materials without a license. Specifically, spraying his fields with Round-up that would have killed everything that was not patented.
You can shrug and say "Oh, it was clearly an accident, Monsanto is evil". And Monsanto is certainly evil. It's just reasonably clear why the judge would view this behavior as deliberate and knowing infringement of a patent.
Yes, the original statement was overly narrow in its view of patents and contracts. Not only should you not enter into contracts that restrict how you can treat your fields, you should also not deliberately act in a way designed to infringe the rights of others if you want to be free to do as you please within the law without incurring liability.
For example, you should not deliberately cultivate a patented plant for which you lack a license from your neighbor's plot of land and then treat it in a way that only makes sense if you're doing that. That will incur liability when a judge notices you are trying to dodge licensing. To put it another way, using processing banned under law.
We shouldn't enforce absurd patents like that in the first place. What's the worst that happens? Some old people starve because their retirement investments tank?
You can shrug and say "Oh, it was clearly an accident, Monsanto is evil". And Monsanto is certainly evil. It's just reasonably clear why the judge would view this behavior as deliberate and knowing infringement of a patent.