I thought there had been a lawsuit against a farmer who intentionally planted a crop near someone else's roundup-ready crop and then bred the resulting seeds for roundup resistance.

Like you, I take the view toward that (potentially hypothetical?) case that the farmer's evident intent to infringe Monsanto's intellectual property is irrelevant because he hasn't done anything wrong. In that case, he is not even party to an agreement, though note that violating a patent doesn't require you to be party to an agreement.