At the end of the day, it does not matter if someone has a seminary PhD or a university PhD. What matters most is the quality of one's work and whether someone can produce. If someone has a PhD from Harvard but can't seem to publish anything, he will be at a disadvantage over someone who has a PhD from a seminary but is publishing a lot. For example, Keith Stanglin published his Calvin Seminary PhD dissertation with Brill. He did not have trouble finding employment.
Harvard, Duke, Princeton and other universities have Divinity schools (i.e. seminaries), which are all accredited by the same institution (ATS). If one wants to teach in public or secular schools, a university degree is paramount. However, if one's pursuits are religious schools, a seminary degree is fine. Though it should be well noted that seminaries do not have the funding universities have.
Ideally, I like dual-doctorates (look at Frank A. James, III), seminary and university, which isn't as intimidating as it sounds, if one pursues a doctorate overseas (i.e. dissertation only). Regardless, whether it is a seminary or a university PhD, one's doctoral adviser is crucial. There is much stigma about religious education in the academy.
I should also add that I have seen some poor dissertations from such prestigious universities as Cambridge, Oxford, and John Hopkins. A university degree does not necessarily equate to quality work. In Antebellum America, the divinity schools ruled the intellectual atmosphere.
As some have said, a PhD is a PhD. The story that Dr. Clark referred to above is a sad depiction of how too many seminaries operate their PhD programs. I know Westminster used to be this way, but I am hopeful that things are changing, and that divinity-school PhDs will make a comeback. I know Lutheran Theological Seminary, Philadelphia, has an impressive PhD program. Those seminaries who offer PhDs too easily should do academia a favor and shut down their PhD programs.
I would be much more comfortable with getting a university PhD in history, as I don't think there is a distinctive Christian approach to history; history is history. When it comes to biblical interpretation and source criticism, I have seen many students get their university PhD only to return with a new-found excitement for all the ways Scripture is fallible and errant. Seminaries have often become cesspools of unbelief because of ill-advised university PhDs.
