I hate to sound like a shill for an evil company, but I've read that even Roundup-Ready crops have an environmental advantage in allowing greater use of low- and no-till methods on industrial farms, which sufficiently reduces erosion of soil (with all the fertilizer that causes algae blooms and other problems) into public waterways. I was stunned to read that a majority of US industrial farms - not only permaculture hippies - now employ such methods.
The general concept is that tilling/plowing is used to mow over weeds, and killing weeds with chemicals is an alternative.
Your question is a good one. I don't know the answer. The articles listed above describe the environmental and health downsides.
A distinct problem - also described in these articles - that may spell doom for Roundup-Ready crops is the emergence of resistant weeds.
There are alternatives to industrial-scale weed control outside of tilling and herbicides. One way is to grow cover crops in the "off season", then cut them and leave them in a thick mat that starves weeds of sun while also gradually rotting and fertilizing the soil, then cut little holes in this mat where you plant seeds. The USDA NRCS promotes methods like this largely through educational programs. Farmers adopt them because they ultimately save costs on herbicides and fertilizer.
Who knows maybe in a few decades we'll produce all food through some industrial process resembling hydroponics, with energy from Nuclear Fusion replacing sunlight, and weeds will be a distant memory.
Upwards of 90% of all major crops (corn, soy, cotton, beets) have BT, HT or both. Other GMO crops and traits are dwarfed by scale of this mass cultivation.