As many other blogs [e.g. Wilde 1 and 2, Marron, M. Nestle] have reminded us since the NYT story two weeks ago (boy, I'm behind!) the FDA has multiple constituents to satisfy. The arm working for citizen health tells us to avoid high fat but the arm helping dairy farmers subsidizes and promotes the consumption of cheese. The two combine in some programs, like WIC (Women, Infants, Children) which directly subsidizes milk products for young mothers and their children [aka many of my friends at church].
WIC is one of the things that would change if we managed to split the FDA pieces up. If what we really want is a supplemental nutrition assistance program run by a health department, we can subsidize fruits and vegetables rather than milk products. If what we really want is a farmer income bill, we can pass that without encouraging overproduction, dumping on foreign markets, or change market prices to support less-healthy lifestyles.
The way things are currently set up, we encourage dairy farmers to breed cows with higher milkfat. The same applies to beef - more marbled beef tastes better, so it sells better. Hog and chicken farmers, however, have seen there is real money in going the other direction and have been breeding the fat out of the animals. Hogs are leaner today than they were 40 years ago. But the regulatory system right now supports less healthy products when they come from cows. Removing or reducing these subsidies and distorting regulations is something both left and right ought to be able to get behind.
That isn't going to win elections necessarily for the good folks who represent cattle states and sit on the agricultural committees, so Congress is probably not the place to look for change here.