Mm... that's a good question. You suppose, too, you could also ask should a Catholic PM have any say in the appointments of the Church of England? However, it's a bit of moot point since I'm pretty sure Gordon Brown has relinquished his (prime ministerial) control over these appointments, hasn't he?

So, hypothetically, I think it would be fair for an atheist to advise from the point of view of still being a good judge of character, morals, and such. In fact, I suppose it could even be argued that an atheist might be more inclined to be impartial than a theist.