Considering the agreement he had signed if anything it was an interesting attempt to vacate that agreement. As in, he attempted the "Patent exhaustion" (first sale) as a means to circumvent paying to use a product. Since there are patent unencumbered varieties available I think its a good decision.

edit: read the NYT article which has further comments by the court, http://www.nytimes.com/2013/05/14/business/monsanto-victorio...

In this case, he sprayed the crop grown from the seed bought from the grain elevator with roundup. This is how everyone knew that it was in fact roundup ready.

It would be interesting to see a case where The seed were used as if they were conventional soybeans, especially if the farmer didn't know that they contained patented genes.

According to my (inexpert) reading of the opinion, it wouldn't matter and the result would have been the same. But maybe there are other defenses that could have been employed if the facts were different. Certainly the policy argument would look a lot different, even if the legal argument remained the same.