I'm not a lawyer, but my understanding is the "seed software" as it existed before you is still free for all to use. The software license analogy would be BSD (any non-copyleft license).

I wonder... if you simply don't use Roundup, the entire process shouldn't be claimed as fair use?.

You are not gaining a profit on the Monsanto work, Those seeds are not provided by Monsanto and as you can not avoid to use genetically contaminated, and identical to other seeds otherwise, you should not face a trial for this.

My understanding is that is exactly how it works in practice. Farmers aren't getting sued for accidentally having a few roundup ready plants in their field; they're getting sued for selecting for roundup ready seeds and then using roundup on their fields.

That's what happened in this case:

  That same year, Bowman applied glyphosate-based herbicide 
  to the fields in which he had planted the commodity seeds
  to control weeds and to determine whether the plants would
  exhibit glyphosate resistance.  He confirmed that many of
  the plants were, indeed, resistant.  In each subsequent
  year, from 2000 through 2007, Bowman treated his second-
  crop with glyphosate-based herbicide.  Unlike his first-
  crop, Bowman saved the seed harvested from his second-crop
  for replanting additional secondcrops in later years.  
  He also supplemented his secondcrop planting supply with
  periodic additional purchases of commodity seed from the
  grain elevator.  Bowman did not attempt to hide his 
  activities, and he candidly explained his practices with
  respect to his second-crop soybeans in various
  correspondence with Monsanto’s representatives.

http://caselaw.findlaw.com/us-federal-circuit/1607718.html

("glyphosate" is the active ingredient in roundup, "glyphosate resistance" is the trait developed and patented by Monsanto.)