POLITICAL THEORY AS A VACATION II:
"These personal experiences and values often provide the motivation to become a social scientist and, later, to choose a particular research question. As such, they may constitute the 'real' reasons for engaging in a particular research project--and appropriately so... From the perspective of a potential contribution to social science, personal reasons are neither necessary nor sufficient justifications for the choice of a topic. In most cases, they should not appear in our scholarly writings. To put it most directly but quite indelicately, no one cares what we think--the scholarly community only cares what we can demonstrate."
-King, Keohane and Verba, Designing Social Inquiry
If you really want to get down into why political theory is ghettoized within political science, I think you ultimately have to deal with the argument of Keohane et al above. In addition to the normative issues discussed previously, I've occasionally gotten something resembling surprise when I express no desire to have whatever work I might do in the future have some deeper societal impact. I'm not against letting your political and ethical positions determine what you study (things must be kept interesting, after all), but I do believe one starts to cross the line when one has not just research interests, but conclusions, in mind before beginning a project, and I think that's a big problem with 'issue-in' analyses. My interest in theoretical responses to fascism and totalitarianism is, in large part, an outgrowth of my own political interests in the same, but I'd like to think that should I do work on humanitarian intervention or liberal anti-communism, I'll be happy to embrace whatever conclusions my sources would cause me to embrace (that is, for example, if it turns out my hypothesis about the allure of authoritarianism for anti-fascists turns out to be false, I'd still like to believe I'd be willing to be wrong and write in support of that conclusion just as forcefully).
Then again, it occurs to me that maybe I was pedagogically raised towards an overly austere belief in what a political science does--many of my professors at Michigan made a big show about keeping politics out of the classroom at all costs, which has maybe skewed my view of what the profession as a whole should be like. Then again, it'd be only one of many ways in which michigan has made me stick out like a sore thumb.