That is the question people are asking in this NY Times piece about a recent geosciences PhD graduate from the University of Rhode Island - a well-regarded school in this field. Marcus Ross is a Young Earth Creationist who submitted his dissertation in paleontology in December and is now teaching at Jerry Falwell's Liberty University. So is it bad thing that the U of RI granted this guy a doctorate? Should they have not let him graduate?
To treat this guy differently would have been wrong. I would be scared by the prospect of universities screening their graduates based on personal beliefs - that would be one more nasty development in the ongoing the balkanization of our culture. We're divided enough already. It would just give ammunition to anti-evolutionists, who would argue that we are using unfair, suppressive tactics because our arguments can't stand on their own.
I'm not worried about Creationists with PhDs because:
1. They're rare, and they will never amass enough numbers to seriously change the balance of the evolution vs creationism fight.
2. They won't have any impact on mainstream science - after grad school, they'll never publish anything that will change the way most professional scientists think about their field. They're not about to get tenure in a science department at Harvard.
3. They're really not more likely to get teaching jobs at public schools than Creationists without PhDs. A YEC with a PhD will probably raise more immediate red flags in the local science community than a less high-profile Creationist. I don't see how the PhD itself would sway anyone except those are are already determined to push Creationism, and for every one YEC PhD there are hundreds of PhDs supporting evolution.
People like this are already out there, but I don't see how they are much worse than Creationists with academic credentials in non-science fields. Has Jonathan Wells, with a PhD in developmental biology, been more of a threat than law professor Phillip Johnson? Articulate, educated leaders of the Creationist movement are going to keep popping up, generation after generation, whether we let them get reputable science doctorates or not. By banning them from graduate programs for their religious beliefs, we would be sacrificing our moral integrity for very little practical benefit.
If people like Marcus Ross do a good job and meet the requirements for a doctorate - that is, if they don't try rig their thesis committee to get away with substandard work, they should be cheerfully given their degrees. Who knows, some of these people may have their faith changed by their work - Ronald Numbers details several such cases, in his book The Creationists (this is highly recommended reading). Not many people can really live with that much cognitive dissonance for very long. And those who can should be allowed to take their degrees and go have a nice fulfilling career at academic holes like Liberty University.