The main criticism that resonates with me is that protected genes like this case are kind of an anti-LGPL, turning naturally open systems into closed ones just by nature of life reproducing via airborne fertilization.
Now this wasn't a great test-case since the defendant was trying to specifically rip Monsanto off, but it is my opinion that it is Monsanto's responsibility to ensure their protected product doesn't spread on its own.
Monsanto developed a mechanism to prevent its crops from spreading by causing them to produce sterile seeds, but it pledged not to use the technology under pressure from anti-corporatist groups[1][2].
I would certainly agree that it is in Monsanto's best interests to ensure their seeds don't spread on their own, if only because the presumption of innocence that must attach to each and every single case they'd try to prosecute.
I know that civil cases have an easier standard of proof but it would still have be difficult to prove every time that a farmer was trying to screw Monsanto over.