There has been an ongoing debate in the atheist/science communities, about whether religion and scientific theories, most often the theory of evolution, are compatible. One one side are atheist stalwarts, such as P.Z. Myers and Jerry Coyne, who claim that believing in evolution is incompatible with religion. On the other side are people like Eugenie Scott, and most recently Michael Shermer. These "accomodationists" claim that there is no conflict, and that "religion [and] evolution can live side by side" as Shermer has claimed in an editorial for CNN. Jerry Coyne has gone on and responded to the article on his blog.
But it seems like the two sides are talking about two very different things. Scientists like Coyne seem to be arguing that we believe the theory of evolution because it follows from the scientific method. And because religion is based on faith and not evidence, religion is incompatible with someone who uses the scientific method, and therefore should believe evolution. And so someone who holds a belief in evolution for the right reasons also should not hold religious beliefs.
The accomodationists, however, are arguing the reverse, that someone who holds religious beliefs can also hold a belief in evolution. If a person who holds religious beliefs begins to believe that evolution is true, does she become more or less rational? If you're already willing to hold beliefs based on faith, it is now possible for that person to hold other beliefs, be it evolution or fairies, and justification becomes almost irrelevant. In that sense, I don't think its any more or less irrational for a religious person to believe in evolution than it is to hold religious beliefs in the first place.
That said, I also don't think scientists should be parading around commending religious people who happen to believe in evolution. At best, those people are capable of scientific thinking, but are unwilling or unable to apply the scientific approach to their religious beliefs. At worst, they are incapable of taking a rational or scientific approach and they believe in evolution for irrational reasons.
Getting everyone to believe in the theory of evolution should not be the goal. It should be scientific literacy, and the ability to think critically. And that is incompatible with holding religious beliefs, if you're willing to apply the same standards to all of your beliefs.