It's not just McDonalds - Go to a grocery store and you see things like this:

Gallon of milk - $3.45
3 liter of soda - $0.59


Fresh organically grown vegetable medley - $2.49/8 oz.
Boxed mac & cheese - $0.49


Soy hamburger patties - $3.89 a box
70% lean ground beef - $1.99/lb

Lean Cuisine frozen entree - $3.49
Banquet TV dinner - $0.99


It's unfortunate that prices for the healthier choices are more, but I'm thinking that is because the healthier choices don't have the load of preservatives that the other things do, therefore a shorter shelf life. That would require special handling, shipping, and processing procedures which would cost the stores more.