Wildlife, imperfections, and disease are a part of gardening life. There are aphids, evil squirrels, scavenging raccoons, crazy winds, and blossom end rot, just to name a few.
For the most part, if a fruit is plucked early enough, some of it might be salvageable. As Colleen Vanderlinden at About.com puts it:
It’s perfectly fine to eat tomatoes that have blossom end rot You can cut away the rotted portion, and eat the rest of the tomato as usual. You’ll want to take a look inside the tomato, because sometimes the rot will extend up into the interior of the tomato a little, even though the outside seems fine. You won’t get sick from eating it if you miss some, it will just taste “off” to you, most likely
Generally, I compost BER tomatoes because they don’t make it to the reddening stage. I don’t want to leave them on the plant to suck up nutrients that the healthier fruits might need. With peppers (yes, even they can get blossom-end rot), I let them grow and cut away any damaged areas, once the peppers reach the desired coloring.
So, would you eat insect or disease -riddled fruits?