Taking John Stewart Seriously

Though John Stewart's business is political satire, I wonder if he hasn't made an important point in noting that the President's opposition to stem-cell research doesn't sit altogether comfortably with his support for his military intervention in Iraq. On the stem-cell front, the President argues that destroying embryos (a bad thing) as a means to saving other human beings (a good thing) is immoral. All sorts of slippery slope-type arguments are evoked to reinforce this point. Yet when it comes to Iraq, the President insists that civlian casualties (a bad thing), although horrible, are unavoidable side-effects of our efforts to promote democracy (a good thing). Thus, in one case doing evil in order to do good is beyond the pale, while in the other it is described as a lamentable side-effect. Now I realize that I'm oversimplifiying quite a bit here but couldn't slipperly slope-type arguments apply just as forcefully in the case of our military intervention in Iraq? Anyone think Stewart is on to something here or is reasoning by analogy in this case the wrong move?