You're all probably thinking that my answer is an unequivocal yes here, but the jury's still out. Fool around with whole-wheat flour for a few days and you, too, will learn that there's a trade off for making things brown. Whole-wheat flour is more dense and will turn even the most delicate of cookie recipes into a scone-like consistency. And I don't mean that in a good way.
My first experiment was an adaptation of a vegan recipe. Vegans, however, don't eat chocolate, since it generally has milk in it, so they supplant chocolate chips with carob chips. That's going too far, even for me, so I used the recipe with real chocolate chips. Three cups of whole-wheat flour (this seemed like a lot; I should have known better) goes into a mixing bowl with a teaspoon of baking powder. Wet ingredients, which included unsweetened applesauce (one cup), agave nectar (one cup), and vanilla extract (two teaspoons) were mixed separately and then integrated into the dry. I used my hands to create the dough and used my hands again to incorporate one cup of chocolate chips and one cup of chopped walnuts.
Wheat flour prevents cookies from spreading, so if you don't spread them by hand (and stupidly, I didn't), what you get is a brown exterior and a play-doughy, undercooked interior. I know that this is more the dough, which seemed too chewy even when I dropped it onto the cookie sheet. I threw the whole batch away.
Pluses of this baking disaster? The batter contains no eggs, which means that you can eat it without fear of contracting salmonella. Also, the dearth of creamable wet ingredients makes this a stand mixer-free recipe, so if you have no dishwasher (yours truly), you'll have fewer things to wash.
Minuses: even if you are a dough-eater, like me, you wouldn't want to eat this gummy concoction. And the cookies were inedible. Truly.
Round two. I decided to adapt the recipe on the back of the Toll House package for healthier purposes. Instead of a combination of white and brown sugars, I used dark agave nectar. Agave nectar is roughly twice as sweet as regular sugar. You have to cream the butter together (yes, in a stand mixer) with butter. Recipe calls for two sticks (otherwise known as 16 tablespoons), so I used 16 tablespoons of Smart Balance, a low-cholesterol butter substitute that very much resembles butter. Smart Balance is salted so I skipped the teaspoon of salt with the dry ingredients. I'm not sure whether or not that was wise. I don't think, however, that salt has anything to do with the leavening properties of baking powder.
Because the agave nectar isn't granulated like sugar, the butter and nectar don't cream together quite right. Oh well. I add a teaspoon of vanilla extract and two eggs anyway. To that, I slowly beat in the dry ingredients that I have mixed on the side: a one-to-one ratio of wheat flour to white flour (two and a quarter cups total) and one teaspoon of baking powder. The dough that forms looks and tastes more like a normal cookie dough. I add the chocolate chips (one cup) and walnuts (one cup) by hand.
I notice, after a few minutes in a 375 degree oven that, once again, the cookies aren't spreading. I guess a cup and an eighth of wheat flour goes a long way. I decided to pull the cookies out and flatten them with the back of a spoon. This worked a little better, but the chips on top got all mangled so that, by the end, they looked more like chocolate chunk cookies than the pictures on the front of the Toll House bag.
They are still a bit doughy on the inside but a vast improvement over my previous attempt at veganism. And by my rough calculations, they come to a paltry 120 calories a pop, worth it if they're yummy and completely not worth it if they suck.
I think my conclusion is this: if you're looking to make pastry healthier, don't. Either eat them or don't, both at your own peril. But making bad cookies is way worse than not making cookies at all.