People's views of pop-up flashes are somewhat misguided. As a professional photographer who owns numerous 580 EX II's and a ton of other lighting equipment, I almost never use the pop-up flash on my 7D...but I have on several occasions found myself wishing I had a pop-up flash on my 5D Mark II. Just by having one, it doesn't mean you have to use it...but by not having it, you don't have the option to, should the need arise. If and when those rare situations come up, it is convenient to have a built-in flash.
You can't always shoot on a tripod or in a studio, and if you don't have your external flash on your camera at that moment, you can miss an important shot. Again, pop-up flash is not ideal, but I wouldn't avoid a camera simply because it has one! While the lighting is harsh and does give a "deer in the headlights" look, I'd rather have a bad photo than no photo at all. This is like when people say that high ISO is useless...obviously noisy high ISO shots aren't ideal, but if and when you absolutely need to capture a shot, it is invaluable.