The trouble is, like most anti-GMO people, you have a fundamental lack of understanding of what genes actually do.
They mutate by themselves for one thing. Should we be running around ensuring that no natural mutations occur? No because that would be an insane exercise and would fly in the face of the fact that DNA has been doing shit for a billion years before you came along to worry about it.
Intermingling crops? Are the crops you're talking about native to the area you're in? Are those crops naturally occurring strains of plants or have they been only in human cultivation for a few thousand years?
I'm not gonna say we _can't_ kill the planet by messing with species, but I will say with the utmost confidence that we won't.