Well, 40k operates according to a version of Finagle's Law; Horus's Law: The Universe tends towards maximum grimdarkness.
Xenos-modified crops would probably not be optimized for human consumption, and vice versa, on the other hand. And Agri-Worlds probably have plenty of strains of them already, and I would bet there's a 'thriving' trade in breeding and selling different strains (10,000 years allows for a lot of selective breeding), especially for any crop designs found in STCs.
Buuuuut. Some xenos crops helping means that the Imperium's hatred of xenos ends up shooting itself in the foot (not in a big way, but enough), which is more grim and dark than if they were completely justified, because hatred without reason (yes there's reason you get what I'm saying though) is darker than hatred with reason.
Some might kill, though I doubt there'd be any temptation to even try them, past the first person dying of food poisoning. Squigs would probably orkify those who ate them, and then grow ork spores in their waste.
Finally...purity is the only way the Imperium can survive. Not the only way humans can.
Question for all of you! If you were to fall to Chaos, which of the Dark Powers would claim your soul? No man or woman is truly immune to heresy. Save for Blanks, of course.
If you're having trouble deciding, here's a few secondary Chaos Gods that can be used to describe mixtures.
Nurgle+Slaanesh (and some Tzeentch, but not as important right now) = Mother Maris, Queen of Nightmares, Goddess of Sleep, Fatigue, and Dreams.
Tzeentch+Slaanesh = Ascalish, God of Experiments, Logic, and Invention
Nurgle + Khorne =
, God of Death, Endings, and Kinship
Tzeentch + Khorne = Malis, God of Betrayal, Anarchy, and Self-Loathing