[warech]

You have the order wrong. Gene alteration + reproduction -> evolution, rather than evolution causing gene alteration. You're right about the rate and general harmlessness of plant evolution, but the gamma ray from outer space is a bit far-fetched. Wikipedia has a nice overview of genetic alteration in plant developmental biology here: http://en.wikipedia.org/wiki/Plant_evolutionary_developmenta..., with a more academic discussion of the effect of polyploidy here: http://www.ncbi.nlm.nih.gov/pubmed/22540042

That being said, I think the fear is that scientists potentially have the motive to create dangerous/unhealthy strains of plants - a motive which miRNA and transposons (god-willing) do not have.