E.g. herbicide resistant genes could be exchanged between domesticated plants and wild weeds, resulting in larger does of chemicals to control the now resistant weeds. New types of weed then emerge that threaten agricultural systems as more dangerous chemicals will now be needed to destroy them. Similarly insent resistant traits might lead to a rapid evolution of pest species.
Moreover, genetic diversity can be reduced as old seeds are replaced by the development of only those seeds that will not be sensitive to the particular herbicide that the seed firm (now often merged with petrochemical and pharmaceutical companies) owns. The economic and ecological consequences thereof need to be considered.
It seems to me the debate is quite a bit more complicated than big versus small, modern vs. traditional, progress vs regress.
Yours, Rakesh