Super Size Me is definitely an inaccurate assessment of how "eating" at fast food restaurant affects you, because Spurlock did not eat like a normal person when he was eating there, and, I believe he reduced his exercise. (According to Wikipedia, he ate an equivalent of 9.3 Big Macs a day -- what normal patron of McDonald's does that?)
As has been mentioned, there are healthy eating options at most places. And limiting yourself to "healthy" options at a fast food restaurant is not substantively different from limiting yourself to "healthy" restaurants. I used to eat the Southwest Salad w/Grilled Chicken (~320 calories), no dressing -- although the dressing is "relatively" okay (~100 calories) as far as dressing goes. It was quick and pretty tasty.
Chick-fil-A's Spicy Chicken Cool Wrap (no dressing) was also a "healthy" dinner for me as well (~420 calories). Unfortunately, I stopped eating at C-f-A due to their political practices.
My old Wendy's dinner was a salad + chicken nuggets + chili. I have no idea how healthy that was, but I will note that it costs me just over $3 and I was a poor graduate at the time. The point here is that, fast food is cheap and is one of the major factors in fast food consumption.
Honestly, I feel more (nutritionally) guilty eating at Chipotle than the other fast food restaurants (and my calorie consumption is definitely higher). But boy, is it tasty.
I don't disagree if you prefer Chipotle from a social perspective (fair treatment of animals) -- but I do find a revulsion of modern food processing technologies on nutritional grounds to be a bit, well, neo-Luddite. Processed foods can be good or bad, depending on how it's processed and writing it off completely I think is excessive. For example, I much prefer my pasteurized milk to the non-pasteurized form coming straight from a cow -- forgive me, if I don't like pathogens in my drinks. (Although I much prefer the refrigerator milk in the US to Parmalat... that's just weird). Cooking is a form of food processing as well and (for better or worse) does help us absorb nutrients (and calories) more effectively than raw food.
At the end of the day, it boils down to the same old adage: "Moderation in all things."