Many problems with your scenario...first of all, commercially grown bell peppers (and other vegetables) are not all of the exact same variety. Sure, there's more popular varieties, but different climates and soils call for different varieties. They use different peppers in California than they do in Minnesota (and it's not just economy of scale - California climate and soil is favorable to bell peppers).
Also, even within the same variety of plant, there are genetic differences, even if they're very similar. A doomsday virus that kills one variety of bell pepper isn't likely.
Also, have you ever looked in a bell pepper? There's a lot of seeds. Should a miracle happen and (say) Anaheim Bell Peppers no longer can be grown, it would be easy for another variety to take its place very quickly. There are seeds banks around the world, private growers, etc. The extinction of most varieties of bell peppers just is not going to happen.
Farmers don't re-seed from their own crops, and (in the first world at least) haven't done so for 70-80 years. So the fact that most farms choose to raise the most popular variety of peppers in a non-factor into the genetic diversity of the crops.