Part of the division into departments is a good thing because it reflects a separation of concerns. A philosophical question (what is our ethical duty as human beings, which methods of argument and reasoning provide valid conclusions under which sets of assumptions, what conceptions of free will are compatible with metaphysical determinism) can't be meaningfully answered from a scientific or artistic approach though scientists and artists are both capable of philosophy to some extent, and in fact it would be good to see academics publishing across related fields more often. I could easily imagine epistemologists, philosophers of science, and scientists productively publishing together in methodology-of-science journals and attending methodology conferences.
Furthermore, departments allow for a deliberate separation of fundamentally incompatible approaches. Some people who take up the dubious academic pursuit of seeing everything from the perspective of feminism or race go to the Women's Studies and Ethnic Studies departments, and the rest of us are often better off without them. If we tried to close or ban the Women's Studies or Ethnic Studies department, people would be taking that crap back into other fields, so as a political compromise we have those departments as a containment field (though I am speaking too harshly, there are certainly benefits for the academics in those fields as well).
To expand on the second point a bit more: one of the virtues of the department model is that (most) departments teach a particular way of approaching problems, a "discipline" if you will. They teach you to "think like a [computer scientist|chemist|psychologist|etc]".
Certainly, there's often a great deal of value in breaking down these disciplinary barriers and attacking the problem holistically - which is why many institutions have interdisciplinary programs and the like. But there's also a value in fields of study retaining some identity as disciplines, with particular methodologies, mores and so forth.
I haven't read the article, but regarding your comment you are treating the departments as if they are completely isolated. I do psychology and it contains many sub-fields such as political psychology, social psychology, biological psychology which basically can be considered as inter-disciplinary fields, bringing these departments together.
I am sure many other subjects have such inter-disciplinary field, sure maths may not go with psychology (although psychologists do need to do statistics) but it goes quite well with physics, chemistry with biology etc. so these departments are not islands on their own isolated from the other fields, each field has much to contribute to other fields.
Furthermore, departments allow for a deliberate separation of fundamentally incompatible approaches. Some people who take up the dubious academic pursuit of seeing everything from the perspective of feminism or race go to the Women's Studies and Ethnic Studies departments, and the rest of us are often better off without them. If we tried to close or ban the Women's Studies or Ethnic Studies department, people would be taking that crap back into other fields, so as a political compromise we have those departments as a containment field (though I am speaking too harshly, there are certainly benefits for the academics in those fields as well).